Category: Chemistry

I commented on a post on the Bad Language blog, produced by my good friend Matthew Stibbe, earlier this week. He was waxing lyrical about cutting power consumption in his SOHO and mentioned how he prefers to brew tea with freshly drawn water. I pointed out that while this may have benefits it would actually increase his kettle limescale problems through the addition of extra calcium and magnesium ions. The effect will be negligible, but if we are adding up every single kilowatt-second then it could make a difference. Of course, brewing tea is not environment friendly in the first place and we should all really be drinking trapped dew under a hessian bivouac, or somesuch.

Anyway, Matthew immediately followed up my comment with a defence of using freshly drawn water for making a cuppa. He’s a man after my own heart. I’ve done this once or twice in the past and it exemplifies precisely how blogs are if nothing else a dialogue (please don’t prove me wrong by not commenting on this post…)

I’d better qualify my boiling/reboiling comment on his blog. Chemically speaking the difference between starting with freshly drawn water each time will be a simple matter of formation of insoluble calcium and magnesium salts. With freshly drawnn water you’re adding new metal ions, which will effectively add to your limescale. However, the de-hardening of hard water by heating is not a perfect process so some will be retained in the beverage once you pour over tea leaves, but the actual balance depends on how soft or hard is your water supply in the first place.

However, now that I’ve had a glass or two of vino (at the time of writing), it has also occurred to me that there are lots of other, organic, components in fresh tapwater, such as humic acids, and organochlorine compounds (possibly even fluorine compounds depending on where you live). These will be presumably be degraded and/or boiled off with the first boil to a degree. In the second boiling it is more likely that you will get rid of all these flavoursome ingredients from the water. So, perhaps there is something in the use of fresh water for the best cuppa, but it’s marginal given that any flavours in the water will essentially be overwhelmed by the flavour of the tea itself. It’s like worrying about the sounds they leave out when compressing a music file into mp3 format.

Meanwhile, the origins of tea lie in an attempt at “storing” water in Asia, so legend goes, and to protect it from contamination by pathogens (namely cholera, although they didn’t know this as the agent at the time). The polyphenolics and other materials in tea infused into the water are to a degree antimicrobial, but perhaps more importantly the simple act of boiling kills of the microbes quickly and succinctly without any recourse to chemistry.

In the “West”, the equivalent solution to the great clean water problem was the addition of fermenting fruits and the subsequent production of wine or beer depending on the region. It’s thought to explain why westerners have evolved an enzyme to break down alcohol and its metabolites whereas some Asians lack this enzyme system.

Given the choice between a freshly brewed cuppa, I know which I prefer, especially at this time of the evening…now where’s that corkscrew?

Most of you who orbit the chemical blogosphere will be well aware of Egon Willighagen’s efforts in helping us build the chemical web. Willighagen is a post-doc at the Wageningen University & Research Center in the Netherlands and cites open source programming as his main hobby.

He runs a chemical blog and founded the all-encompassing Chemical Blogspace (elementally designated Cb). For this month’s Reactive Profile, I asked him about his work, the next big discovery, and about the highs and lows in running Cb.

You can read the complete interview in the April issue of Reactive Reports.

Also on offer in RR this month:

Super Insulators – Superconductors, materials with zero electrical resistance, have been known for decades, but their counterpoint materials, the superinsulators, could transform materials research and electronics design.

Gator Aid – Biochemist Mark Merchant of McNeese State University in Lake Charles, Louisiana, has investigated a range of proteins found in gator blood that might one day be used to fight serious infections.

Fake Bird Flu Drugs – International health organizations are lying in wait for the emergence of a form of avian influenza that could spread between people and lead to a global epidemic, killing millions.

More reactive chemistry…

The Periodic Table of the elements is a fascinating icon of science. It is incredibly useful and has been exploited and sexploited too in the form of a periodic table of yoga and a sexy PT. It has also been hacked apart, cut and paste into different formats, created as illuminated wall cases, woodworked into furniture, spiralled, spherized, and generally rebuilt in almost every imaginable way ever since Mendeleev first dreamed of laying out his elemental cards according to the periodicity of elemental properties.

Now, in an effort to inspire chemists to reconsider the foundations of the periodic table, chemical philosopher Eric Scerri of the University of California, Los Angeles, is building a new way to classify the chemical elements one step at a time.

Writing in the latest issue of the Journal of Chemical Education (PDF 2008, 85, 585-589), Scerri explains how the periodic table initially arose from the discovery of atomic weight triads but he now suggests that chemists should recognize the fundamental importance of atomic number triads.

This sea change in elemental attitude might enhance the periodic table by classifying the elements at a fundamental level as basic substances. As such, he and his colleagues have developed a new version of the “left-step” periodic table, which looks very different from the conventional PT. In the new layout, with its step-like pattern actinides and lanthanides are no longer relegated to a standalone box, but form the first step of the PT.

Climbing right to the transition metals (Fe, Mn, Ir, Sg et al) on the next step and then to the non- and semi-metals, such as boron carbon, oxygen, silicon etc and finally a step in which the halogens (fluorine, chlorine…), noble gases (neon, xenon…), alkali metals (potassium, sodium…) and alkaline earth metals (beryllium, calcium…) form the final highest step on the right. Hydrogen tops the halogen column and helium crowns the noble gases rather than acting as the outer beacons as with the conventional layout. (Click the graphic for a clearer, full-size view).

“The left step table has been around for some time,” Scerri told me, “but I am modifying it to accommodate two atomic number triads which would otherwise be absent. They are He, Ne, Ar which ceases to exist as a triad in the usually encountered left-step table and H, F, Cl which does not exist either in the conventional medium-long form table or the usually encountered left-step table.”

In the grander scheme of things, whatever form the Periodic Table takes in the future matters not to those of us who sing, so we end with a song, the periodic table song from Tom Lehrer (who was 80 on April 9, 2008 and gets a mention in the Official Google Blog this week), known simply as The Elements.

In my ChemWeb Alchemist column this week, German chemists have constructed nanoscopic balls from DNA, researchers in the UK have discovered natural antibiotics in Greek cheese that could prevent food poisoning, and Stateside, researchers have developed a low-pressure hydrogen storage material that might pave the way to a hydrogen economy (if we want it). I also report on ancient color in statues and relief as well as another chemical scare story. This award in this issue represents more than four decades of surface science and was presented to UCB’s Gabor Somorjai at the ACS meeting.

There’s cancer news over on SpectroscopyNOW this week with my report on findings suggesting a link between raised heavy metal levels and cancer, whether or not it is a cause or an effect of a change in metabolism in cancer is not yet known, but it represents a new avenue in research.

I also report briefly on a review of the state of the art in determining the absolute configuration, the definitive shape and structure of organic molecules using special add-ons for NMR spectroscopy and X-ray crystallography. Speaking of X-rays, in the XRD ezine, I report on the recent work from the Pyle group at Yale University who have unravelled some of the secrets of DNA’s message bearing cousin, RNA.

Finally, I got a chance to use a couple of my gun photos, which are heavily Photoshopped images of a toy gun, in a piece on forensic science and the problem of gathering hard evidence now that ammo has gone lead-free.

Chemspy users may have noticed a few outages recently, at least on the blog section of that site, so rather than spend many an hour trying to upgrade servers, I’ve decided to re-host just the blog content from that site on Sciencebase. The databases and chemical search tools will remain in place over on that site. The following is a small selection of recent items about informatics, online science tools, and drug design, which will hopefully be of just as much interest to Sciencebase readers.

• DBpedia for Chemists
• Drug Design on the Playstation
• Google Science Dot Com
• Open Notebook Science
• PaperID – An Open Source Identifier for Research Papers

I’ve imported all Chemspy blog content as it stood on April 4, 2008, so you can access the Chemspy archive in the Sciencebase chemspy category. Hopefully, the few dozen Chemspy posts won’t stream into the RSS feed, doesn’t look like they have yet, as they’re all simply date-stamped with their original post dates dating back to early 2007. Apologies for any glitches. At some point, I will migrate the Chemspy newsfeed over to Sciencebase too, so please subscribe to the Sciencebase feed (there is a chemistry category) to keep up to date with Chemspy updates.