Chemistry Department Blog

Whilst such titles are normally followed by the exploits of inorganic chemists, 2011-12 sees the dawn of a new computing facility within the department. The new supercomputer, known as the IB-Server is the result of a 7 research group collaboration with resident computing officer Jörg Saßmannshausen. The project, begun in 2010, will allow group members sole access to 420 cores with fast ‘Infiniband’ connections, dramatically shortening calculation times and enlarging the molecules and systems that can be investigated.

IB-Server joins the 5 pre-existing chemistry computer clusters in calculation for a wide range of projects. UCL has a long and excellent research record in computational chemistry, from crystal structure prediction (Professor Sally Price), to the modelling of selectively oxidative catalytic surfaces (Professor Nora de Leeuw). The impacts in terms of theoretical understanding, programming and contributions to on-going experimental investigations have been significant. Countless other computational researchers will benefit from IB-Server but the machine should also have a wider impact. As Dr Saßmannshausen explains, computational chemistry is a useful tool at the disposal of the whole department. Not only can computational screening highlight areas for further experimental research, but modelling allows insight into sometimes ‘unintelligible spectroscopic data’.

The cluster itself comprises of 40 boxes each housing 4 nodes, with each node having 4 dual core ‘Intel L5630’ processors. The key feature though is a low latency ‘Infiniband’ connection allowing swift transfer of data between nodes. The effect of the connection is exemplified by the recent benchmark test carried out using the CP2K code; on the gigabit network a standard calculation took two and a half days, whereas the new IB-Server machine reduces the calculation time to less than 12 hours. Benchmark test results also placed UCL chemistry computers above ‘HECToR’, the UK’s leading academic computational research facility. Practically, the reduction in calculation time will greatly increase throughput for parallelised codes such as ‘VASP’, ‘CASTEP’ and ‘Quantum ESPRESSO’ (all implementations of Density Functional Theory) and will allow much more challenging systems to be studied.

As use of the departmental clusters increases, Jörg’s role in keeping the machines functioning correctly will be supplemented by consolidating the data backup system and providing areas for the department’s keen code writers to store programming projects. One single entry point for the UCL computational chemistry community to access programs and support for new users are also being considered. In the meantime, chemists needing a chemist’s advice on programs, implementation and hardware have expert help available.

- Jane Yates

Last Tuesday brought to the Chemistry department a group of 20 inquisitive Year 9 students and their parents for a CO₂ workshop. The afternoon aimed to let these students explore the properties of carbon dioxide inside a lab and inform them how dangerous this molecule can be.

Students and parents alike split into groups and began experimenting with a bowl of dry ice, a bottle of bubbles and the glove they had been given.  Aiming to demonstrate the properties of carbon dioxide a group of volunteers lead experiments including putting dry ice into a lab glove to watch it expand as it turns from a solid into a gas, blowing bubbles over the bowl of dry ice to demonstrate the changes in density and finally allowing dry ice to melt on a paper towel to show that CO₂ is never a liquid- the paper towel never gets wet!  After a tentative start the students really began to grasp the theory behind the experiments and a couple even came up with their own experiment by releasing the CO₂ gas from the glove into a stream of bubbles to see if they sank.

The experiments ended with a display to the group of how carbon dioxide acidifies an alkali solution via the simple act of adding dry ice to a gigantic test tube of water with indicator solution. This reaction captivated its audience as the addition of the ice caused the water to bubble and smoke whilst the solution green to reddish orange in colour.

Our afternoon ended with a talk from Dr David Rowley, who built on the group’s existing knowledge of global warming, explaining why Earth is the best planet for our survival and calculating the Earth’s temperature.  Analysing atmospheric CO₂ levels from the last 10,000 years and answering questions such as “why is the sun yellow?” Rowley outlined correlations in the rise of carbon dioxide and fossil fuel use, as well as the effect this has had on the Earth’s average temperature. Although so far these temperature increases have been small, can mankind really want to find out what a further increase could do? After all, prevention is always better than cure.

-Olivia Lynes

On a sunny winter’s afternoon a group of UCL’s chemists arrived at the King William IV pub in Leyton for some purely ‘academic pursuits’. We were greeted by a roaring fire and Dr. Louise Price’s other half, who’s enthusiasm for ‘Brodie’s Beers’ led Louise to organising the tour of the brewery for UCL Chemistry’s real ale drinkers.

Two pints (a steal at £1.99) later we were off on our tour of the brewery which was just next to the pub, in a large cold shed full of large metal tanks. Our guide proceeded to explain their brewing process, telling us about the various experiments in the creation of new and different tastes and aromas of the beers, whilst enthusiastically producing bags of hops for us to sniff. Following this we traipsed back into the warm pub for a beer tasting of 4 of the 13 beers on sale.

Brodie’s brewery is named after the James and Lizzie Brodie who took over this east London brewery back in 2008. Their tasty beers proved so popular they’ve now expanded to three pubs in London and their beers are soon to be distributed across England and Scotland.

Where to drink Brodie’s brews- Head down to one of their central London pubs – The Old Coffee House in Soho and The Cross Keys in Covent Garden. Alternatively, a beer festival is being hosted at the main pub King William IV at 6-9^th April.

 

-Clair Chew

Two of UCL’s PhD students Aisha Rahman and Marion Brooks-Bartlett were shortlisted to participate in the AkzoNobel (a Dutch chemical company) poster competition last Monday. Up against stiff competition from Cambridge and Bristol universities, they were to present their ideas on “Tomorrow’s Answers Today”, with their entry focusing on hydrogen fuel from photocatalytic water-splitting.

The event began in the AkzoNobel boardroom in Victoria by meeting the Research Development and Innovation (RD&I) Communications Leader and the Communications Officer. Then, in ‘The Apprentice’ style the participants were whisked away in black cabs and driven like VIPs to the Holiday Inn Mayfair hotel and finally wined and dined at the Sofra restaurant.

The next morning was filled with running through lines, from the room to the breakfast table, until finally they were on their way to the Royal Society of Chemistry’s Burlington House, where the competition was due to take place. Here the contestants presented their pitches and defended their posters for an hour of questions from managers, directors and customers of AkzoNobel; amongst them were five anonymous judges for the poster competition.

Aisha and Marion were runners up of the competition, but the CEO and the Executive Committee Member of RD&I were so impressed with the level of the presentations that everyone received a cash prize and they personally expressed how much they enjoyed Aisha and Marion’s presentation in particular.

Marion said of the experience, “Overall we would say- a fantastic event! Great experience and a great opportunity to represent UCL. I would encourage anyone to take the opportunity to apply for competitions when they arise- you never know how far you’ll get if you don’t try!”

- Marion Brooks Bartlett

Prof Jim Anderson and student Rafael Bou Moreno have got themselves the cover of Organic and Biomolecular Chemistry with an article: Synthesis of ureas from titanium imido complexes using CO2 as a C-1 reagent at ambient temperature and pressure DOI: 10.1039/C1OB06576A
Nice picture of Battersea power station too.
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Simon Mayo, BBC Radio 2′s late afternoon DJ,  made a flying visit to the Department yesterday as the Graham lab was used as the location for the filming of some school science demos. With Southampton Outreach Officer Jonathon Speed they set off a classic “Whoosh bottle”, some Elephant’s Toothpaste and a Gummybear (shown below).

Anyone concerned that our smoke detectors might be faulty can relax. Crosby Medley, our Graham Lab supremo, capped them off in advance to avoid embarrassment.

Videos should be up on the Radio 2 website later today – we’ll update this page later.

Those are the words on the Olympics motto. They are meant as a challenge for the world’s top athletes. But not for David Cowan, director of the drug control centre (the anti-doping facility for the london 2012 olympic and paralympic games) and the head of department of forensic science and drug monitoring at King’s college London, to him these words present to him a different Olympic challenge. “Faster analysis, Higher sensitivity, Stronger proof”. Proof to catch out drug abusers competing this summer. He delivered a stern warning to potential cheats at the CPS meet last Tuesday: “ To the person who thinks they can beat our test, WATCH OUT”.

A mind boggling combination of chromatography and mass spectroscopy is used to isolate the tell-tale signs of various substances. This means that any cheeky spoilsports wouldn’t be able to predict what their spectra will look like and therefore wouldn’t be able to mask their cheating vices.

The massive operation of testing every athlete (increase testing from 25 to 425 per day) during the Olympics is a joint effort between pharmaceutical giant GlaxoSmithKline and King’s College University’s Drug Control Centre. GSKs involvement allowed a satellite laboratory to be built near the games just off the M20. This is not just any laboratory, it has to be accredited by the World Anti-Doping Agency. One of the methods of accreditation is a “secret shopper” test keeping David on his toes.

Professor Cowan believes that most athletes do not want to take drugs and cheat. He believes that the London Olympics can be a drug-free games and reiterates his warning as the finale of his talk:

You’ve been warned…

Cheats keep out! 

-Clair Chew

http://www.kcl.ac.uk/biohealth/research/divisions/aes/research/drugcontrol/index.aspx

It’s that time of year again; the start of a new term when we say “Happy New Year” to all of our students. For UCL Chemistry 2011 is an exciting year in which  we have one of the biggest clutches of new starters ever.

We have over 100 first years with some of the highest grades ever, 23 Master students (drawn from both the M. Res. and M.Sc. in Energy) and 55 doctoral students from the Eng. Doc. and Ph. D. programmes. With 80 Natural Scientists and about 300 Life Science students, all of whom have to do at least some Chemistry here in the Department things are exciting and busy. It’s going to be a good year – a time to work hard and play hard too.

 

Claire Skipper, a second year graduate student with Prof. Nik Kaltsoyannis, won this year’s GSK Travel Award. The prize, sponsored by GSK is given on the basis of a seminar to the Department. In a close run contest in front of 150 members of staff, students and postdocs, Claire, a computational chemist, won with a talk entitled: “Transition metal, hydrazine linked hydrogen storage materials. The first computational study of the Kubas interaction using the quantum theory of atoms-in-molecules“.

The other excellent talks were given by James Sayer (Tabor Group) (A flexible synthetic approach to bicyclic heteroaromatic compounds as ATPase inhibitors),  Rozie Sarip (Hogarth/Sankar Group) (Gold molecular clusters to nanoparticles: a bottom-up approach to supported nanoparticles for applications in heterogeneous catalysis), Paul Koovits (Anderson Group) (Development of a reductive nitro-mannich reaction and work towards an asymmetric variant), and Roman Spesyvtsev (Fielding group) Ultrafast internal conversion through conical intersections in aniline.

The award provides funds for a second year postgraduate student to travel to a conference abroad.