Chemistry – Page 24 – David Bradley

Medline on Facebook

For those who care about such things as online social networking, and if you’re reading this blog, I assume that could be you, there is now a Facebook application available that allows you to cite your journal publications (provided they are listed in PubMed).

You can add the Medline Application (yes, I realize PubMed and Medline are not synonymous, but that’s the name the authors used) – by following this link.

I’ve added a few of my publications from Science, Nature RDD, Drug Discovery Today and PNAS, they’re listed towards the bottom of my profile below my Flickr gallery.

Chemical Language Translated

During my time at the Royal Society of Chemistry (do I sometimes make it sound like a prison sentence?), I watched in awe as my old mucker Andrew Wilkinson helped reformulate the IUPAC book of chemical definitions commonly known as the Gold Book. That mighty auric tome is online and searchable with a click these days. And is as useful as ever to chemists looking for a quick description for a jargon word.

Take chiral, for instance: “Having the property of chirality“. Hmmm. So, look up chiral: “The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind.” Such a crisp and easily comprehended definition. Not.

Obviously, there is a need for technical definitions, but somtimes such definition simply complicate something that could be just as easily described often with a single word. Chiral = handed. (The clue’s in the word itself, which comes from the Greek for hand and I’m pretty sure the scientist who coined the term did so to save us all the trouble of talking about non-superimposable mirror image objects (you know, like hands and gloves?). Indeed, many a chemistry student would grasp the concept much faster and many a lay reader of a scientific paper would understand if such terms were explained in parallel with their simpler analogue. So, for all you non-chemists, here’s a Boxing Day list together with links to their technical definitions if you need the fully Monty,

Chiral – handed
Hydrophobic – water hating
Hydrophilic – water loving
Micelle – microscopic bubble
Cyclodextrin – starch rings
Mass – how much stuff
Isotope – same element, different mass
Bond – a link between atoms
Organic – made with carbon
Inorganic – made without carbon
Lipid – Oily or fatty natural molecule
Morphology – shape
Half life – Time taken for value to half
Second Life – Virtual meeting place

Obviously, these simple definitions gloss over the finer details, but isn’t that the point of a glossary? “Professionals often face difficulties explaining these terms to lay people because they are too aware of the exactness of the concept, emphasizing both the morphological and functional aspects,” says chemist Andrew Sun, recently interviewed in Reactive Reports. There are many more I use in writing for a non-technical audience, but some jargon words are quite stubborn. Are there any good, simple definitions for the following?

Polymer
Sublime
Catalyst

Chemistry’s Sun Rises in the East

Many of you will know chemist Andrew Sun from his On the Road blog and from his occasional but insightful comments on the Sciencebase site. I recently interviewed him for the Reactive Reports chemistry webzine and you can read the result there in the current issue. I edited his answers to fit the magazine for length and housestyle but I’ve reproduced his full answers to one or two poignant questions here exclusively for Sciencebase readers.

How do you think being a chemist in China differs from working in “The West”?

I don’t know very much how people doing chemistry in the west. I get an impression from videos of lab work posted online. But one difference I am very sure is that we do not have enough money and we do have a poor academic system. Most students still have to pay tuition at the MS stage. The campus scholarship can only pay for a dinner with your friends, and we have far fewer, or no, third-party scholarships here). In the PhD phase public subsidies can still hardly cover the cost of living. Bosses (supervisors) cannot be too nice to their students because they are also running out of money. To apply for more funds and get promoted in a badly designed academic system they have to publish enough papers in high quality journals. They have to publish more in less time so they need more unpaid PhD students working harder.

China pours the world’s second largest bucket of money into science according to statistics, but one should also consider the fact that no NMR machines, no TEM, SEM, AFM sets, neither other instruments, are manufactured in China. Bosses have to buy these from abroad (CNY 1.00=USD 0.13=EUR 0.10, plus taxes) – and regain the cost by charging several hundred per sample for characterization requests. (Cryo-TEM, which is widely used in the study of soft matter, cost CNY 2000 per sample here!) Money thus goes two ways to both buying the instruments needed and to paying the usage fees.

In addition we have a weak chemical industry here which cannot provide qualified reagents. So to conduct a delicate synthesis with less failures in less time, one trick is to buy your reagents from Alfa Aesar, Sigma Aldrich, etc. who charge your boss more. Not to mention the local glassware – we cannot find any tight ground glass joint from local manufacturers. Oftentimes PhD are forced to manipulate impure reagents in a leaky glove box, with minimal budgets to test their products for sure, yet still having to publish in journals with high impact factors.

As such PhD students in China are a depressed group and we hear of suicides among PhD chemists from time to time (in one case the poor guy synthesised a few milligrams of potassium cyanide and…). That’s why now lesser MS grad students are moving on to a PhD. In fact most of the MS students aren’t truly working for science; they are only working for the degree which could mean a slightly better salary than a BS degree in the job market. So most MS students go to find a job once they get their degrees, and yet a large number pursue their career of science abroad. So we have the brain drain problem – obviously the above mentioned situation in China is not attractive enough of them to come back in the future.

However I’m still hopeful because everything is getting better, not worse. Therefore I chose to stay in China during my PhD period.

What more can chemists around the world do to work towards a global chemical community? How might certain more restrictive governments be persuaded of the benefits of such international collaborations?

First it is important for them, both the chemists and the governments, to realize the benefits of international collaborations; not only why, but practically how. Currently with limited communication, for example, a US scientist can hardly know why he/she should cooperate with a Chinese scientist for a project. More communication and understanding between chemists from different countries are needed to start any collaboration. The growing online chemistry community could provide such chances. But currently Chinese chemists who actively participate in the online community are rare; I know no one else except me.

Governments might consider much more, for example the ‘leakage’ of knowledge or secrets. However I believe the advantage of collaboration can outweigh the shortcomings which can be overcome by carefully designed policies and contracts. I guess the Chinese government should welcome global collaborations because we are currently much weaker and have a lot to learn from others. But currently the extent of this is much smaller than I’d hope for. There is still much to change.

For more Reactive Profiles, grab the site’s chemistry interview feed.

Don’t Poison Your Dog This Holiday

Theobromine structure

‘Twas the night before Christmas, when all through the house
Not a creature was stirring, not even a mouse

Well, that may not be quite true, do you know what your dog is doing right now? What about the cat? They’re not rummaging through the presents under the tree are they? You didn’t leave any luxury plain or dark chocolates under there did you? If you did, you could wake up to a quite horrible surprise when Christmas morning comes around. Chocolate makes pets ill! That’s the important seasonal warning being delivered by vets everywhere.

Poisonous chocolates So, what’s the problem? Surely a little chocolate snack in the night isn’t going to harm good-old Fido? Well, our vet begs to differ and so do the veterinary toxicology sheets for the chocoholics’ favourite fast-food. Man’s best friend, and several other animals, you see lack a particular liver enzyme that their owners do possess, that breaks down a toxin found naturally in chocolate – theobromine.

Theobromine has nothing to do with the element bromine, rather it is a bitter alkaloid from the seed of the cacao tree, known scientifically as Theobroma. The basic chemical skeleton is a xanthine unit, same one on which several other more well-known natural chemicals are based. The stimulant caffeine (from coffee beans) is a xanthine, for instance, so too is theophylline (found in tea and used in treating COPD and asthma).

Non-chocolate Labrador

Lacking the enzymes to metabolize theobromine leaves dogs exposed to the toxic action of the compound, which can cause vomiting, diarrhoea, hyperactivity, tremors, seizures, abnormal heart rhythms, and in extreme cases death.

So, what are the first signs of chocolate poisoning, what’s the lethal toxic dose, and what should you do if you think your dog has been at the chocolatier’s produce? Well, the first signs of chocolate poisoning are vomiting and diarrhoea, increased frequency of urination, and nausea. A toxic dose that will cause symptoms is about 100-150 milligrams of theobromine per kilogram of body weight, toxic dose could be approximately 250 and 500 mg/kg. A kilogram of milk chocolate will contain about 2 grams of theobromine. So a greedy, little dog is at greater risk of a serious digestive upset than a big gluttonous dog if he or she snaffles a 250 g bar of milk chocolate.

There is no direct way to treat chocolate poisoning in dogs, although inducing vomiting if the animal is caught “brown-pawed” (best left to the vet) is probably a good idea. A dog that has eaten a lot of chocolate will almost certainly require hospitalisation for at least the four days while the theobromine is naturally excreted (It takes about 17 hours for a dog to excrete half of the theobromine in its system, which means this toxin will reach vital organs repeatedly via the blood stream). But, who needs that, or worse, at Christmas? As they say: a gram of prevention is worth a kilo of cure.

For lovers of cats (small, domestic, big, wild) keep the aspirin out of reach. It’s deadly poisonous to felines.

December Chemical Discoveries

In addition to my interview with Chinese chemist Andrew Sun, mentioned earlier this week, the December issue of Reactive Reports features the pick of chemistry news

DNA Nanorings A simple approach to making rigid DNA nanorings with tailor-made functionality has been developed by Michael Famulok and his team at the University of Bonn, Germany.

Sunshine Superpower In the depths of the Northern winter, as we approach the shortest day of the year, what could be more welcome than a little sunshine news.

Five Firsts in Chemistry With 2007 rapidly coming to an end, the inevitable lists are popping up. Not wishing to be left out this holiday season, the American Chemical Society has compiled a Top 5 from its own publications. Oh, and by the way, Sciencebase didn’t want to be left off the wish list either, so I did a Top Ten Molecules of 2007 item just recently.

Composting Chitosan Cat-litter Composite

Spectroscopy Now

That has to be the oddest blog headline I’ve come up with this week, but it’s not in fact that esoteric once you get down to it. Basically, researchers in China have created a new material based on dolomite (porous kitty litter material) and the crab shell derivative chitosan.

The new composite material not only absorbs water it can release an NPK (nitrogen, phosphorus, potassium) fertiliser over a prolonged period for use in agriculture and horticulture. Advantages are, improved irrigation efficiency and less run off into waterways together with improved crop yields. More on this, in my SpectroscopyNOW column this week and you get a chance to see a photo of my kitty too. What more could you want? Other than links to the rest of this week’s news in SpecNOW, of course.

In NMR news, a brainy approach to using microNMR coils could allow scientists to probe the activity of cerebral compounds, such as choline, without having to worry about NMR’s relatively low sensitivity. In the X-ray ezine, I report on how British scientists have demonstrated that it is possible to predict the crystal structures of small organic molecules using software, winning them accolades at this year’s Blind Test in Crystal Structure Prediction, organised by the University of Cambridge and hosted by the Cambridge Crystallographic Data Centre.

Finally, new informatics evidence suggests that the land-bridge which is currently the Bering Strait was the sole route into the Americas for humans tens of thousands of years.

WiChempedia Coming Soon

It seems it’s now public knowledge that WiChempedia is on its way thanks to Tony Williams at ChemSpider and his colleagues.

“Over the past few weeks I have had a few discussions with a member of the ChemSpider Advisory group regarding a concept to create WiChempedia. I’ve enjoyed these conversations with Alex Tropsha (professor and Chair in the Division of Medicinal Chemistry and Natural Products in the School of Pharmacy, UNC-Chapel Hill),” says Williams in his latest blog post.

Over the past few weeks Williams and his colleagues have been looking at the quality of data on Wikipedia and trying to figure out the best way to mash ChemSpider’s efforts with those of the WP:CHEM team. “Our intention is to deliver wiki-capabilities in ChemSpider and to use the Open Content associated with chemicals and drugs on Wikipedia inside the system,” Williams says, without, he adds, reinventing the wheel or offending the Wikipedians.

“My intention as we work through downloading the data and to check, validate and correct what is sitting on Wikipedia directly for benefit to the community,” adds Williams.

Volcanoes, Moons, Pearls, and Alchemy

Moon (Photo by David Bradley)

This month’s physical sciences Spotlight over on the Intute site turns on oceanic plans, lunar volcanoes, and pearl necklaces:

Infertile Global Warming Plan – Plans to fertilize the oceans with iron or other nutrients in order to absorb atmospheric carbon dioxide and so ward off global warming are not viable according to a report from researchers at Stanford and Oregon State Universities.

Buckyball Pearl Necklace – A new type of polymer material made by stringing together the tiny football-shaped fullerene molecules has been synthesised by chemists in Spain. Under the microscope, the material resembles a string of pearls.

Volcanoes of the Moon – Even though astronauts have set foot on the Moon, analysed its surface and brought samples back to Earth, we do not yet fully understand the Moon’s origins nor how it has evolved during the last few billion years since its formation. New clues have now emerged from a study of the Moon’s past volcanic activity that suggest that volcanic activity began 4.35 billion years ago (+/- 0.15billion), a relatively short time after the formation of our planet’s biggest satellite.

And, in ChemWeb’s The Alchemist newsletter: Small-scale chemistry with a variety of applications that could improve not only healthcare but the environment has led to the Small Times innovation award going to Louisiana Tech’s Yuri Lvov, The Alchemist hears this week. Also in chemistry news, old anticancer drugs could be repurposed for treating genetic blood disorders sickle-cell anemia and beta-thalassemia.

A barrel of fun is to be had analyzing wine barrels for dioxins and polyaromatic hydrocarbons, while laser light has been found to switch vanadia films from reflective to transparent without heating, a possible boon for optoelectronics applications. Finally, in this week’s Alchemical selection, holy double-helical nanorings of DNA with single-stranded gaps have been engineered by German scientists while US researchers have demonstrated that pouring millions of dollars and tons of iron into the oceans may not have the desired effect on reducing atmospheric carbon dioxide levels after all.

Googling for Genes

Those clever people at Harvard are using Google‘s API to allow users to search for gene sequence fragments on the Web in combination with a text query. You’re limited to 1000 searches per day and have to enter your own API key to get the maximum benefit. But. that’s probably enough to be going on with.

From the site: Query Gene is distinctive because it is not limited to a single database. Instead it captures genetic information across the net using Google. It works by taking a gene sequence in combination with other search terms, finds similar sequences using NCBI’s MegaBlast, retrieves the descriptions of those matching genes from NCBI’s Entrez Nucleotide database, and performs a series of Google searches using the combination of your original search terms and each gene description. The percent sequence identity is indicated alongside each match: this indicates how much of your queried sequence is contained in the sequence it matches.

You might want to find out what disease states are associated with a specific nucleotide sequence. No problem. Paste in the sequence and enter a text phrase, such as “genetic disease associated with” and up pop the results. Well, actually, they didn’t with the test I tried, but that could be down to my browser configuration. I got “Sorry, we are under maintenance: Please try again in a few weeks”.

A sample sequence is given here. If someone else could confirm or refute the maintanance outage for ChemSpy readers that would be very helpful.

Sciencebase Top Ten Molecules of 2007

Graphene

Everyone loves a list. (Don’t they?) Well, as we’re approaching the end of the year and some of us are well into the panto and party season already, I thought it would be a good idea to run down a hit parade of this year’s molecules. So, here’s the Sciencebase Top Ten Molecules of 2007:

10 – Graphene – chicken wire carbon sheets hit the headlines this year and will continue to do so as researchers learn more about this unique material’s optical and electrical properties. One day, carbon may even replace silicon as the elemental of choice in computing.
9 – Helium – at the time of writing physicists in Canada had taken an important step towards understanding supersolidity in helium, stretching it a bit to include this in a list of molecules. This new state of matter forms at very low temperature and under extreme pressure and now it has been found that cooling makes supersolid helium even stiffer.
8 – DNA – deoxyribonucleic acid, and more specifically, the deoxyribonucleic acid that resides in every cell of genomics pioneer Craig Venter. The J Craig Venter Institute claims that this “Independent sequence and assembly of the six billion base pairs from the genome of one person ushers in the era of individualized genome-based medicine”.
7 – Water – Good old H₂O continues to confound those scientists hoping to explain its anomalous properties, as supplies of the fresh stuff will dwindle as the century moves on, it’s heartening to know that close to absolute zero, water exists in yet another phase.
6 – Ethanol – a seasonal favourite, of course, the active ingredient in so many beverages. As with a certain other molecule in this Top Ten, this year there has been a lot of hot breath resulting from various and conflicting health studies on the effects of ethanol on human health, expectant mothers and their unborn children, and others. So…raise your glasses to ethanol!
5 – Rotaxane – 140 years ago, Scottish physicist James Clerk Maxwell devised a thought experiment that might help scientists break the law. An entirely legal, molecular version of Maxwell’s Demon made its debut this year, thanks to chemists at Edinburgh University.
4 – Azadirachtin – After decades of trying and countless post-doc and grad students have come and gone Steve Ley at Cambridge University finally published a total synthesis for the natural insecticide azadirachtin.
3 – Epothilone – could the anticancer drugs produced by soil microbes finally have come of age with the announcement from pharma giant Bristol Myers Squibb that it has obtained approval in the US for semi-synthetic analogue of epothilone B against drug-resistant metastatic breast cancer.
2 – Carbon dioxide – this year, there has been more hot air produced around this greenhouse gas and climate change than I care to cite.
1 – Hydrogen sulfide – yet another small molecule with a big impact. Scientists recently discovered that H₂S could be the key to longevity, at least if you’re a nematode worm. A study published in PNAS in December demonstrated that the “rotten egg” molecule increases heat tolerance and lifespan in the molecular biologist’s favourite, Caenorhabditis elegans

Well, those are my choices, I deliberately avoided looking at Science to see what they’d come up with for their Molecule of the Year, before I put this post together. If anyone has their own Top Ten or even just a Number 1 let me know.