Spring 2009

Aerosol particles and lung disease The changing face of physical science The dynamics of protein systems Half a century in Lensfield Road As I see it...

Former head of department Jeremy Sanders has a new role within the university – he’s now head of the school of physical sciences. He tells Sarah Houlton what the job entails

What does the new job involve? research councils, channels a growing year since 2003! It’s hard to have the I am responsible for eight departments, amount of its research funding to areas really big strategic creative chemical which makes up about a fifth of the uni - that it deems to be important, be it cli - ideas now as I don’t spend enough time versity’s activities – chemistry, physics, mate change, energy, health related, or in serious thinking, but when someone earth sciences, material sciences, pure whatever. gives me results I can see the implica - maths, applied maths, astronomy and And the university needs to learn how tions and what the next step should be, geography – plus the Isaac Newton to manage these large research initia - because I can draw on more years of Institute for Mathematical Sciences. The tives in such a way that we retain the experience than I care to admit. And school is the layer between the central classic Cambridge freedom of the indi - there’s still no greater pleasure than sit - university administration and the indi - vidual to discover the unexpected, ting with a few of my group and being vidual departments. In the past, it was quirky, astonishing things that are trans - able to interpret an nmr spectrum better mainly a conduit for communication formational. That’s the big challenge in than they can. and money between the centre and the our local culture. If you look five or 10 departments, but in the past year it’s years into the future, what’s the appro - been given a lot more executive author - priate departmental structure to enable s r ity, so I am officially the budget holder this? And what’s the appropriate man - e for all those departments, which agement structure to enable it to happen d n amounts to about £150m a year. in the best possible way? a S

So is it responsible for overseeing There must be other strategic y teaching in those departments? decisions you have to make. m e

Since last year, the schools of physical and Oh yes – decisions about buildings – r biological sciences have had joint respon - which departments should move, and e sibility for the natural science tripos, so when, and where, and how it is all J all our teaching now officially reports to funded. So I haven’t escaped from build - me and my biological counterpart. Prev - ing work! But the pleasure is that it’s V iously, teaching within the departments mostly long-term thinking. This is actu - C reported to the university through a ally what heads of department ought to pretty undefined route, but it’s now got a be able to do, but rarely get the time to formal governance structure, and the – spend time with colleagues thinking schools will take strategic charge. strategically about where we want to be There’s a huge education agenda here in five or 10 years and how we go about because in future we will have to ensure it, rather than having to spend one’s there is a better horizontal integration of time, as the head of department undergraduate teaching between the inevitably does, dealing with day-to-day individual subjects in the natural science short-term problems and crises. Born: London; grew up in Hackney and tripos (NST). With geography and And it’s not all management stuff: I’m Wandsworth maths, which are separate but overlap finding it very enjoyable as there’s actu - Status: Wife Louise is a former biologist. wiht NST, there are more and more ally more science in it than you might Their son David is an assistant professor of multidisciplinary courses that need to expect! As head of school I am involved physics in Mexico City, and daughter Deb is a be managed. In addition, there is the 4th in every professorial appointment, so I college administrator in Oxford. year teaching, which is Part III in some am exposed to a wonderful breadth of subjects, an MPhil in others, and in a science from cosmology and astronomy Education: Jeremy spent seven years at few cases it’s also the first year of a PhD. to high energy physics, through geogra - Wandsworth comprehensive school, then In some areas, you can imagine the phy and conservation, nano- and bio - studied chemistry at Imperial College, before same lecture course being used for all materials with, of course, chemistry at moving to Cambridge for a PhD with Dudley three purposes. So it all needs to be ver - the heart of it all. Williams. tically integrated, as well as horizontally Career: After a one-year postdoc in This may soon lead to the formation of Does this give you more time to pharmacology at Stanford in the US, he a graduate school for physical sciences, do chemistry? returned to Cambridge in 1973 and joined which would oversee postgrad education The next few months are rather busy as the academic staff in chemistry as a across the school – admissions, training I am also currently a deupty vice-chan - demonstrator. He’s been here ever since! courses, and all the other non-research cellor, overseeing the university’s 800th Interests: Cooking (he says he solves all his functions. That’s a big job for the school, anniversary celebrations until the end of problems toiling over a hot stove) and music, and I’m ultimately responsible for it, 2009. So at the moment I do very little of the classical variety. although I have a newly appointed direc - teaching – you can’t do everything! But tor of teaching who is responsible for it I do still make time to see people from Did you know? Football is not on Jeremy’s leading the changes. my group almost every day, though they list of talents. He was last seen on a football do have to have appointments as I can’t pitch back in 1971 playing for the Dudley What about research? just drift up to the lab every evening as I Williams group against Alan Battersby’s Increasingly, the role of the school is to used to. I’m seeing as much of my group. ‘Dudley only had a group of 10, so we develop a long-term research strategy, group as I did when I was head of all had to play, as did he, to make up 11,’ he recognising that research funding these chemistry, and I lik to think I’m able to says. ‘I think they would probably have played days tends to come in larger and larger give them more ‘quality’ time. I pub - better with only 10 men – without me!’ aliquots. The government, through the lished more papers last year than in any

2 Chem@Cam Spring 2009 Reluctant reactions Letters

Chromic cleaning

Dear Editor, Roger Ward’s exhibition, shown in your Autumn 2008 edition, made me (1967-70) feel out of date too! But where was the large yellow mixing bowl of chromic acid whose role was vital in removing ‘intractable tars’ from expensive and often hand-blown glassware? No bench was complete without it. Lab 287 (Steve Quarrie I think) devised the Chromic Frog (a sort of paper boat made of Kleenex) which had to char within half a second for the mixture to be considered adequate. Happy (if rather messy) days. Dr Peter B Baker 9 Kenilworth Road, Ealing, London W5 5PB

Out of date?

Dear Editor, Well, thank you for reminding me that the work I did at Then and now… We’ve been in Lensfield Road for 50 years, and Cambridge is ‘hugely out-of date’. I spent my first year in the building looks a little different these days. Read more on p9! the chemistry department in Pembroke Street and recall the subsequent move to Lensfield Road as an introduction to the promised land. Intimations of mortality came some years later when I saw apparatus that I had used in my working life in the Science Museum in London. Confirmation of the relevance of your reminder is indi - cated by my favourite page in your admirable journal being on the back. Yours sincerely, Roger Duffett

Spit and polish

Dear Editor, I think I was among the first wave of undergraduates to move from Pembroke Street – where I had spent my first two years doing practicals – to Lensfield Road where everything was pristine. Benches were cleaned meticulously, I polished on a Saturday morning (as a research student) – something that seemed to be expected! Yours sincerely, Bill Collier Silverdale, 28 Seaton Down Road, Seaton, Devon

Cover This newsletter is published three times a year by the Chemistry Department. Opinions are not necessarily those of the editor, the department, or the university. Editor-in-Chief: Steve Ley Editor: Sarah Houlton Photographers: John Holman, Nathan Pitt, Caroline Hancox Contents Editorial Board: News 4 Brian Crysell, Bill Jones, Jonathan Goodman, Research 7 Rosemary Ley, Jeremy Sanders Glass blower extraordinaire Address: Alumni 11 Phil Gallego in fiery action Chem@Cam, Department of Chemistry, University of Cambridge, Lensfield Road Chat lines 12 Photograph: Cambridge CB2 1EW Nathan Pitt and Caroline Hancox Phone: 01223 763865 Puzzle corner 15 email: [email protected] website: www.ch.cam.ac.uk

Chem@Cam Spring 2009 3 News

Two chairs filled Matt wins Lilly award… We’ve made two new professorial appointments in the Matt Gaunt has won the Eli Lilly Young past couple of months. First, Clare Grey is to take up the UK Lecturer award for 2008. The award is Geoffrey Moorehouse GIbson chair of chemistry. Oxford given annually to a lecturer who has been graduate Clare is currently in the chemistry department an independent academic less than five at Stony Brook University in the US, and takes up her years for their achievements in chemistry. appointment here in the department in July. Clare Matt was appointed as a lecturer here in studies and develops new materials for batteries, fuel Cambridge in October 2006, with a Next cells and catalysis. Generation Fellowship funded by Philip and Patricia Brown. And Professor Shankar Balasubramanian has been The award involves a cash prize, and appointed as the Herchel Smith Professor of Medicinal Matt has to give a lecture at the Lilly Chemistry, a joint appointment with the clinical school. research site in Earlwood, Surrey. ‘I was Already a professor within the department, Shankar’s only there to give a lecture last year, so work focuses on the chemical biology of nucleic acids. they’re going to get another dose of me ‘I am delighted by the excellent appointments that have already,’ Matt says. ‘I’ve promised to give been possible to these prestigious chairs,’ says head of them a different talk this time!’ department Bill Jones. ‘The filling of these posts provides Meanwhile, Matt’s very excited that great opportunities for the department in the very he’s just had his first paper in the jour - important areas of energy and medical research. nal Science. The paper was about Matt’s work on substitution reactions on aro - matic rings, where the substitution takes tion at the ‘wrong’ place by using a cop - place at a position on the ring you per catalyst instead of the more usual Homerton’s new status wouldn’t expect. First year undergradu - palladium. Chemistry teaching fellow Deborah ates learn that if the ring has an elec - ‘We’re really excited by these results,’ Longbottom holds a joint post at tron-donating group on it, the substitu - he says. ‘We hope that the technique will Homerton College, which has just been tion will happen at the ortho and para allow all sorts of organic molecules to given permission to apply for a Royal positions. Matt’s found that he can make be made in a simple reaction that would Charter as a full college of the university biaryl compounds where the substitu - otherwise take many steps,’ he says. in its own right. Homerton was at first exclusively a teacher-training establishment, but it …and Robert a Syngenta prize has been accepting students for natural sciences since 2001, during which time Robert receives the College has established a solid base his cheque from of fellows in a range of scientific sub - Syngenta’s jects, including Deborah, who joined in Andrew Plant October 2007. The college has been on the Cam - bridge map since 1894, and its staff and students have been members of the uni - versity for more than 30 years. However, as an Approved Society, until now it has been governed by trustees, but now the college – the largest in Cambridge – will become self-governing and take its full place within the university. ‘It’s a very exciting time to be part of Homerton College,’ Deborah says. ‘And I’m really looking forward to making a Robert Phipps, the PhD student with make, and what data to request. ‘As the positive contribution in the future.’ Matt Gaunt who’s working on the project data came back, another round of deci - described in the Science paper, has won a sion-making would be required, and Deborah: excited to be part of prize himself – a Syngenta postgraduate after about five or six iterations, each Homerton as it scholarship in organic chemistry. group presented their final molecule,’ takes its full Syngenta selected about 20 applicants he says. ‘Following this, the scientist place in the to participate in a three-day assessed who actually led the discovery of the university workshop at their site in Jealott’s Hill real agrochemical the study was based near Bracknell. ‘It involved activities on revealed its structure, and the ration - such as one-to-one interviews with ale that led to it.’ staff, making a poster of your PhD work In the end, six of the participants – in 30 minutes before presenting it to including Robert – were selected for the Syngenta staff, and group tasks such as scholarships of £1,000 in cash and a retrosynthesis and agrochemical discov - further £1,000 to pay for a trip to a sci - ery,’ Robert says. ‘This task was a sort of entific conference. simulated discovery of a successful agro - ‘I’ve submitted an abstract for the ACS chemical, but accelerated to fit into a conference in Washington DC this single day.’ August,’ he says. ‘I found the workshop In small groups, they were given lead really enjoyable and engaging – and of structures and had to make important course it was great to win one of the decisions such as which analogues to scholarships.’

4 Chem@Cam Spring 2009 www.ch.cam.ac.uk 800 years in colour In 1209 a group of dissatisfied scholars disappearing into a black hole. The left Oxford and settled in a small market highlight of the show was a series of town just south of the fens. The sketches by the renowned illustrator University of Cambridge has decided Quentin Blake, showing Newton and his that this event marks its foundation, and apple, and Darwin in the Galapagos. so this year we are celebrating our In July, we will be holding a party in 800th Anniversary. This celebration is the Botanic Gardens for 10,000 quite separate from the fund-raising University and College employees and development campaign. their families, and a few days later a BBC The theme of the year is Transforming prom concert will be given over to a Tomorrow: Cambridge transforms the musical Cambridge festival. people who work and study here, and it A host of other activities, initiated by transforms the world through the ideas staff and students, and sponsored by the that it produces. We opened the year 800th anniversary committee, have with bell-ringing and a spectacular light threaded throughout the year, providing show on the walls of the Senate House entertainment and education for all ages and the Old Schools. The light show, and interests. A football match between which was seen by over 10,000 people Cambridge United and Oxford United during three rather chilly January raised over £3000 for Camfed, our char - evenings, was a pageant of Cambridge ity of the year, which provides educa - t s r history and achievements. Notable sci - tional opportunities for girls in Africa. u h

k entific highlights included the DNA All these activities, which are c u

L double helix, green fluorescent proteins described in much greater detail at l e

g inside cells (pioneered by Roger Tsien, www.800.cam.ac.uk, are masterminded i N

: who worked in the Department in the by a great team headed by Geoff Morris. o t o 1970s and shared the 2008 Nobel Prize I merely chair the steering committee. h P in Chemistry), and Stephen Hawking Jeremy Sanders

Salt is best in cooking! Brian enthrals the audience

A recent Chem Comm from their structure. Poly-L-gluta - The second Alex Hopkins Lecture was Jonathan Goodman, and col - mate forms a tight helical given by our own Brian Johnson to an leagues at Unilever and the conformation in the pres - appreciative audience of more than 200 Max Planck Institute in ence of salt, whereas it people during this year’s Science Festival Leipzig, was highlighted on stretches out in pure water. in March. the journal’s cover, perhaps Proteins play an important Alex was a much-loved teaching fel - because of its important culi - in giving food its texture, low at Churchill and Fitzwilliam, who nary implications. and Jonathan wants to know was also a mainstay of inorganic teach - Thanks to some complex how they interact with other ing in the department. His father John molecular dynamics simula - components of food, such as helps us to celebrate Alex’s life by sup - tions, it appears that salt fat and carbohydrates. porting an annual lecture, which is sup - doesn’t just affect food’s ‘We want a better under - posed to relate chemistry to everyday taste, but its texture as well. standing of the interactions life and contain an element of humour. They found that only a tiny between proteins and the Brian’s lecture title was ‘Small and amount of salt is needed in other components,’ he says. beautiful’. He took us on a gentle jour - t t an aqueous solution of pro - ‘This may help increase the ney through symmetry and philosophy, i P

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teins to have a big effect on quality of processed foods.’ before turning to modern catalysis. a h t

Starting with the platonic solids and a N

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neolithic sculptures based on them, he o t o

moved on to the hexagonal symmetry h of snowflakes, and Kepler’s (possibly P apocryphal) realisation that six apples on a table arranged in a hexagon around spellbound. Towards the end, he even a seventh might hold the clue to the managed to introduce some catalytic fundamental organisation of chemistry from his own research. snowflakes. It was to be 300 years The department is already thinking before X-ray crystallography confirmed about next year’s lecture. Please send any this idea. suggestions for potential lecturers to The audience spanned the genera - Jonathan Nitschke ([email protected]) tions, from the children of a member or Jeremy Sanders. of staff to an enthusiastic 90-year-old I Science Week was a resounding suc - pupil in the art class that Brian teaches cess again this year, with more children in his ‘retirement’. than ever visiting the department to get Brian, in his unique and apparently a taste of what chemistry’s all about. spontaneous fashion, drew the audience There’ll be lots more about it in the into his presentation and kept them Summer edition of Chem@Cam !

Chem@Cam Spring 2009 5 News

The short summary of Cambridge’s results are that we had the largest proportion of 4* (top Assessing chemistry research rated) work. All panel members were, of course, excluded from discussion of any institutions For much of summer 2008, while most sensible and Jeremy Sanders to the panel of wise men – where they had major conflicts of interest. folk were relaxing through the long sunny and one wise woman – who rated the research Jeremy, who chaired the panel, said, ‘The RAE evenings or were enjoying their latest exciting of 31 submissions by 33 universities; Eastchem panel were a great pleasure to work with: hard- research results, 16 dedicated members of the and Westchem were joint submissions by working, well-informed, scrupulously fair and chemistry RAE panel were firmly attached to their Edinburgh and St Andrews, and Glasgow and with a good sense of humour to leaven the pro - hot CD readers. Not music, not audio novels, and Strathclyde respectively. ceedings. The panel were pleased to see how certainly not raunchy videos, but 4,900 pdf doc - Meeting in rain-soaked Lake District hotels well UK chemistry has performed over the past uments containing the ‘outputs’ submitted by over or in the sterile environment of the 18th floor few years. 1,200 academics in UK chemistry departments. of the notorious Centre Point in London, they ‘However, it is extremely frustrating that Each output was read by at least two panel mem - debated, discussed and eventually pronounced HEFCE’s funding model and the broad spread of bers, which meant everyone read an average of their verdicts. The masochists amongst you can scores across the higher education sector generally more than 600 outputs, together with pages of sta - read all the results (and the very carefully writ - have meant that chemistry departments in tistical data and departmental strategy documents. ten minutes of all the meetings) at England have mostly ended up with less funding Cambridge chemistry contributed Steve Ley www.rae.ac.uk/pubs/2009/pro. next year, despite their good performance.’ A golden celebration!

December’s end-of-year head of depart - ment’s talk was a little different from normal – it also included talks from Presenters in action... Clockwise Brian Crysell, Tony Kirby, Ian Fleming, from the right: Brian Crysell, Ian Smith and David Watson looking Tony Kirby, Ian Fleming, Ian back at the history of the Lensfield Road Smith and David Watson labs and some of the people who’ve worked here in the past. You can read what Brian, Tony and Ian Fleming had to say in this issue – and see photos of the building under t t construction – starting on page 9. And i P

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Ian Smith and David’s presentations will a h t be featured in the next issue of a N

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Chem@Cam . Watch this space! s o t

It was followed by the staff Christmas o h party – check out the photos on p14. P The Corporate Associates Scheme Arecor Thanks to the generosity of the depart - networking events at the department; Heptares ment’s Corporate Associates, we have I Access to emerging Cambridge Astex Therapeutics been able to benefit the education and research via conferences, special brief - Illumina Astra Zeneca environment for students and staff. For ings and various publications; example, the Associates pay for univer - I Access to the department library Johnson Matthey Catalysts Asynt sity-wide access to SciFinder Scholar and photocopying/printing facilities; Lectus Therapeutics and ChemOffice. They also make signifi - I Regular communications about Biotica Technology cant contributions to the library for upcoming events and colloquia; Maruzen International Boehringer Ingelheim Pharma journal subscriptions. Moreover, they I Subscriptions to department publi - provide exam prizes, faculty teaching cations, including Chem@Cam; Merck Sharp & Dohme BP I awards and summer studentships, and Priority notification of and free Novartis BP Institute have recently funded the refurbishment access to departmental research lectures; of a state-of-the-art meeting room with I Ability to hold ‘Welcome Stalls’ in Pfizer Bristol-Myers Squibb teleconferencing and display facilities. the department entrance hall; Corporate Associate membership not I Preferential conference rates; Proctor & Gamble Cambridge BioTechnology only provides essential support for the I Free access to the teaching lectures Roche Cambridge Medical Innovations department, but also provides numer - held within the department; ous benefits to help members work with I The full services of the Corporate Sigma-Aldrich CambridgeSoft us and achieve their business objectives. Relations team to facilitate interaction Members enjoy many benefits through with students, staff, and other parts of Society of Chemical Computing Group their enhanced partnership with the the University of Cambridge to help Cornelius Specialties department, such as: achieve your corporate objectives. Chemical Industry I Visibility within the department; If your organisation would be inter - Takeda Cambridge Dr Reddy’s Custom Pharmaceutical I A dedicated meeting room and ested in joining the Corporate Associates Services office for members to use while visiting Scheme, then please email Jane Snaith at Unilever the department; [email protected], or call GlaxoSmithKline I Invitations to recognition days and 01223 336537. Uniqsis

6 Chem@Cam Spring 2009 Research

Aerosol particles are important in the atmosphere – not only do they reflect and absorb sunlight, but they are also The chemistry of aerosols trigger the formation of clouds. Each raindrop forms around a tiny aerosol particle. ‘The process isn’t very well Atmospheric aerosols have a big impact on the climate, but they understood,’ explains Markus Kalberer, aren’t well understood. Markus Kalberer is trying to find out more whose research centres on atmospheric aerosols. ‘But aerosols have a huge impact on the climate, and we want to know more about them, and what effects they have on health.’ The chemical composition of these aerosol particles – which are nanometre sized – is complicated. About half of them are inorganic, like ammonium salts, or salt near the sea, and the remainder are organic. ‘These are a “soup” of many different chemicals, and more than 10,000 have been identified so far,’ Markus explains. ‘We’re looking at how these organic aerosol particles are formed and what they’re made of, and looking at new analytical methods so we can investigate them more closely.’ t t i P

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HEALTH PROBLEMS a h t

Aerosol particles in the atmosphere are a N

: thought to have negative health effects o t o and exacerbate respiratory diseases such h as asthma. The classic example is the P London smog in 1952 when an extra aerosols that form outside fairly well,’ That’s the erate effect – we deposited simulated 4000 people died in just one week. he explains. ‘We flow the aerosols we instrument they smog particles, and it would have been Since then, it’s been established that make through the instrument onto the use to test aerosol astonishing if the cells had just died!’ he there’s a correlation between death rate lung cell culture, which mimics the nat - particles on lung says. ‘So far we’ve focused on healthy and concentration of atmospheric parti - ural way they are inhaled and deposited cell cultures on cells, but the next step is to use diseased cles smaller than a couple of microme - on the surface of the lungs. If we’d col - Markus’ screen! lung cells – healthy people don’t have tres. ‘There is most likely a causal con - lected the particles on a filter, extracted problems in smog, but those with respi - nection between the two, but what is so them with a solvent and pipetted them ratory problems do.’ harmful about these particles is not onto the cells, we would lose the He’s also using analytical techniques known’ he says. aerosol nature. It also means that the to study the complex mixtures of One of the projects Markus is work - reactive components of the aerosol, organic chemicals that make up atmos - ing on looks at the effect of aerosol par - such as radicals and peroxides, remain.’ pheric aerosols. Taking just one chemical ticles on lung tissue. ‘We are collaborat - Initial results show that the particles – alpha-pinene, which is given off by ing with biologists who look at the bio - do indeed have an effect on the cells – pine trees – and oxidising it with ozone, logical responses and inflammation that macrophage white blood cells do their the result is a mixture of about 400 dif - aerosols cause on lung cell cultures,’ he job and consume the aerosol particles. ferent compounds. ‘If you allow the says. ‘We have built an instrument that The biologists have also looked at reaction to carry on for a few hours, allows us to direct aerosol particles onto whether the macrophages still work then some of the products are acids and cell cultures without having to collect after they’ve taken up the particles, and di-carboxylic acids, which have very low them or process them.’ it turns out their activity is lower so they vapour pressures and spontaneously In the longer term, they plan to use have been affected by the aerosol depo - form aerosols,’ Markus says. ‘And in the the instrument – it’s small enough to be sition. They also found that they release aerosol particle, further reactions take portable – in a real world setting, but chemicals called interleukins, which is place, so in just a couple of hours all they’re already getting interesting part of the inflammation process. these different compounds are made.’ results in the lab. ‘We can mimic the ‘It’s a good thing there is only a mod - He’s interested in finding out what components of these aerosols could be

r Born: in Basel, Switzerland Career: In 1999 he moved to Caltech for an having an effect on health, and is using

e 18 month postdoc with atmospheric chemist r Status: His wife Petra is a PE teacher and analytical techniques to investigate. ‘By e sports therapist. They have an 18-month-old John Seinfeld. He returned to ETH for a using mass spectrometry, for example, b l daughter, Aline habilitation position (a little like a research we can look at how many of the com - a fellowship) at the end of 2000, and moved to

K pounds are peroxides or acids,’ he says.

Education: A degree in environmental science Cambridge as a lecturer last October. s at ETH in Zürich was followed by a PhD with ‘We’ve developed a method that allows u Interests: Spending time with his family, us to quantify the total peroxide con - k Heinz Gäggeler at the University of Berne and r skiing (sadly not in Cambridge!) and travelling. tent, which is very variable over time.

a the Paul Scherrer Institute close to Zürich. ‘His I’d now like to look at the concentration

M main interest is in discovering super-heavy Did you know? As an undergraduate, he was elements, but he also uses aerosol techniques also interested in geology and spent two of radicals, which will be challenging as for analytical purposes, which over the years summers on a German research ship, sailing some of them are very short-lived. We

V developed into a research direction involving from Hamburg to Brazil and western Africa to have to develop a very rapid method C aerosol processes in the atmosphere and that’s take sediment cores – a far cry from his that allows us to sample the air and what I was working on.’ current interest in the atmosphere! analyse the radicals before they have had chance to react.’

Chem@Cam Spring 2009 7 Research The dynamics of protein folding

Proteins fold up into complex shapes and arrangements that are vital to their function. Justin Benesch is looking at the dynamics of the folding process

Proteins are long, flexible chains of amino acids which have to fold up in the right way if they are to work cor - rectly – many diseases are a result of misfolded proteins. One of the ways that nature goes about ensuring the folding process is done properly is by using ‘molecular chaperones’, which t t i

help prevent these errors occurring. A P

n lot is known about how these house- a h t keeping proteins achieve this, but much a N

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of this information looks at specific t o snapshots in time. Justin Benesch is h P interested in finding out more about what’s going on in real time. function,’ he says. ‘Their structures are huge protein assemblies together in the ‘I’m interested in the dynamics of pro - very poorly defined because they are gas phase like this!’ tein assemblies,’ he says. ‘It’s not just the difficult to study with conventional On a basic level, the information from way they put themselves together – do techniques, primarily because of their a mass spec is just a mass, but curiously, they fall apart again, how do they inter - dynamic quaternary structure, but we’ve Justin says, it can actually tell you a lot. act with other assemblies, and what tran - found that mass spec is very helpful.’ ‘In the first instance, the mass is unique. sient shapes do they go through while Mass spec’s big advantage over other Counter-intuitively, the larger and more they are folding? Determining these fluc - techniques such as x-ray crystallogra - complicated it gets, there are fewer tuations is often even more difficult than phy or NMR is that it’s possible to look things it could be. If you’ve got a mass determining the structure itself!’ at large protein assemblies over a very of 18 it could be water or ammonia, for He’s using mass spectrometry to look short period of time. ‘Crystallography is example, but if you’ve got a very big at what’s going on with one class of the “gold standard” for determining the mass of, say, a million, and you know chaperone, the Small Heat Shock structure of protein assemblies, but first what the constituent units are – which Proteins. ‘They aren’t very well under - you have to grow a crystal, which might for proteins you do, of course – then stood at all, but it appears that their take a couple of weeks, and it’s very you can work out what combinations of dynamics are an essential part of their hard to trap out intermediate states dur - those units you could have that would fit ing the chaperoning process,’ he says. with the mass that you measure.’ Born: Vienna, to an East German-Austrian father ‘You might get a snapshot at one point, This, effectively, gives a ‘signature’ and an English-Austrian mother. Moved to but not an idea of what’s happening in mass for the protein assembly, which h real time. And with NMR, though recent means that Justin can look at how it

c Switzerland – where his parents still live – aged 5

s advances have made it hugely exciting changes over time. ‘I’m really interested

e Education: After an English primary school in in the study of large assemblies, it can in the reactions these proteins undergo n Geneva he went to boarding school in England, e still take hours or even days to get a and the pre-equilibrium states they go and then to Oxford to study chemistry. He moved B

strong enough signal-to-noise ratio, traverse,’ he says. ‘If you mix two pro - to Cambridge for his PhD with Carol Robinson, at n

i which can hinder getting any informa - tein assemblies together and they inter -

t the same time as she made the move tion on pre-equilibrium states.’ act, you can get information about what s Career: A one-year discipline hopping postdoc u It only takes a couple of minutes to is going on. We’ve mixed two different

J fellowship with Carol and electron microscopist run a mass spectrum, so it’s possible to small heat shock proteins together, and Helen Saibil at Birkbeck College was followed by a get information about dynamics. First, found that they swap elements between further postdoc with Carol. He was appointed a the protein is dissolved, and the solu - themselves. This is easy to spot as the V Royal Society URF in October 2008 tion put into a gold-plated glass capil - masses we observe for them change, C Interests: Unusually for an Austrian, he’s a keen lary. It’s then sprayed out into the mass and as we know the masses of the dif - cricketer – and plays for the physics department! spectrometer by pushing it through the ferent components we can get an idea He also loves cooking, photography and skiing. capillary with a gas and an electric field, of what is changing.’ ‘Although I’m pretty anglicised, when there’s which gives a spray of protein within If you just looked at one protein on skiing on the TV I’m completely Austrian,’ he says. solvent droplets. its own, then you would never know Did you know? Justin thinks he may have been ‘It’s the same principle as spray- that these reactions were going on, he involved in the construction of the largest sausage painting a car,’ Justin says. ‘The solvent says. ‘But it turns out they do, and they ever made in Cambridge, for his house-warming then evaporates under vacuum, and happen very quickly. We’ve found that party last year. It was a Cumberland ring-style you’re left with naked protein ions in with some disease-related mutations in sausage, about the same size as a kettle barbecue, the spectrometer. I remember when I human proteins this exchange process and was about 6.5m long unravelled, weighing first started learning about the tech - is much slower. So we have to wonder about 7kg. ‘It was very heavy, and it was rather nique I was really surprised that the how important these intrinsic dynamics difficult to turn it over!’ proteins don’t just fall apart in the spec - are to the proteins’ function, and we trometer, but you can actually keep plan to look at this in the future.’

8 Chem@Cam Spring 2009 History Half a century in Lensfield Road In December, we celebrated our 50th anniversary in Lensfield Road. Brian Crysell, Tony Kirby and Ian Fleming look back at the history of the department, and what it was like in the late 1950s

fessor in Manchester, was invited to accept the 1702 chemistry chair. He vis - ited Pembroke Street and was shocked and disgusted at what he found. Not only had Cambridge become one of the weakest chemistry schools in the coun - try but the laboratory, still lit by gas, was ‘a disgrace to any University’. Todd made six conditions under which he would consider the appointment, one of which was that a new laboratory would be built on a new site as soon as possible after the end of the war. The Lensfield Road estate had been owned by the University for many years. It comprised the villa Lensfield House, and a cottage in quite substantial gardens, and was once home to the architect William Wilkins who had designed much of Downing College, parts of Kings, Trinity and Corpus, and also the National Gallery in London. Although the Scott Polar Institute had Brian Crysell on the history successor should wait until after the Above: The old already been built in part of the gardens Although chemistry has been taught in Second World War was over, and a com - Pembroke Street of Lensfield, it was still a large site and Cambridge since about 1682, it wasn’t mittee should run chemistry in the chemistry building much favoured by Todd and the until 1888 that the first purpose built interim. Several important contribu - Secretary General of the Faculties. University Chemical Laboratory, in tions to the war effort were made in The architects for the new laboratory, Pembroke Street, was opened. In its day, Pembroke Street, including a continua - Easton & Robertson, and work began on it was one of the finest in the country. It tion of the work on gas warfare, photo - the site in 1950 with funding from the was lit by gas, and fire precautions were graphic emulsions, corrosion and lubri - Below left: the old University and government grants. Steel quite primitive. Much work was done cants and also, of course, explosives. labs were lit by rationing made progress very slow and during the First World War on chemical One of the least publicised projects was gaslights; below the project was completed in four stages weapons research under the direction a team working on the separation of right: Lensfield over a period of almost 10 years. Stage of Professor Sir William Pope. plutonium and uranium isotopes as a House, the villa one, incorporating organic, inorganic After his death in 1939, it was contribution to the Manhattan Project. that once stood and radiochemistry, was completed in decided that the appointment of his In 1944, Alexander Todd, then pro - on the new site 1956, and the move from Pembroke ­

Chem@Cam Spring 2009 9 History

­ Street began. Stage two, physical and Above: Excavations theoretical chemistry, was finished in on the Lensfield 1958, and the was building officially Road site; right: opened by Princess Margaret on the construction November 6th that year. Stages three gets under way and four, the teaching classes and the large lecture room were not completed Tony Kirby quent chemistry departments that were until around mid-1960, when the old remembers built after the war! lab was finally vacated. Ian and I came up in Although the building was officially What is now the Bristol-Myers 1956, just before opened on 6 November 1958, parts of Squibb lecture theatre was designed as the new building in it had been in use to some extent before the centrepiece of the new building. Lensfield Road was then, and when we first saw it the con - Not only was it to be the largest lecture completed. Alex - struction had still to be completed. The room at that time in Cambridge, but ander Todd, who arrived in 1944, was north and south wings were complete, also a cinema, theatre and concert hall. crucial in the development of this but various parts such as the teaching At the back was a fully equipped projec - building and the department, and we labs and east wing were yet to be built. tion suite for both 16 and 35 mm films. still feel the benefits today. The car park was also full of houses – it The blackboards and screen could be He was very influential in the scientific was very different from how it is today. lowered into a pit to reveal a stage, com - establishment, which helped in securing Classes were gradually moved from plete with dressing room facilities off to the funds to build the new department. Pembroke Street to Lensfield Road dur - both sides. The bench at the front could Although he never said how much had ing the late 1950s. The Part I lectures for be disconnected from all the services been spent, the word at the time was that the Natural Sciences Tripos were still in and wheeled out in sections to create an it cost about £4m – rather a lot of money Pembroke Street in 1957–58, and cer - area for a small orchestra. in those days. The story also goes that the tainly all the practical classes were still Sadly, these extra facilities gradually Universities Grants Commission were there as the labs in Lensfield Road were became less used and eventually most of horrified at what they had agreed to, and not ready. That year Part II classes were space they occupied was re-allocated. halved the specifications for any subse - taught in both places. No expense was spared to ensure this room was aesthetically correct, to the extent that the grain of the seats run the Below: the steel same way as the desktops, and each frame that gives individual seat was reinforced with the building its metal rods to ensure they do not snap strength; right: the when they are sat on! labs semi-finished

10 Chem@Cam Spring 2009 Chat lines

The building was officially opened by Princess Margaret, who’s pictured right with Lord Todd

The teaching itself was also in transi - being lectured to by Bernard Saunders or tion. John Harley-Mason, Malcolm Barry Kipping, who ran separate courses Clark and Peter Sykes were at the van - side-by-side, and your director of studies guard of the new chemistry. The subject chose one or other for you; Tony and I was changing in the way it was taught both went to Kipping’s course. and researched, and we were the bene - After two terms of organic, we had ficiaries of these enthusiastic young one on inorganic chemistry in the Easter people who had been brought into the term, taught by Alan Sharpe. The differ - department by Todd. ence between the two was dramatic. Furthermore, he had brought in Kipping taught traditional chemistry – Harry Emeléus into inorganic chemistry functional group chemistry, starting from Imperial College in 1945, and he materials, products and reagents, and tion, with Christopher Longuet- had made a big impression – as had nothing in between – no explanations at Higgins. His goal through the 50s and Christopher Longuet-Higgins as a theo - all. Sharp introduced us to electrons, to s into the 60s was to get across to the retician. Theoretical was already rela - and p orbitals, and we began to see how world the importance of molecular tively strong as Lennard-Jones was the periodic table came out the way it orbital theory - thinking about how already in position, originally as did, which was a revelation! electrons were distributed and moved as Plummer professor of chemical science, The next year, again, we had very tra - the basis of organic chemistry. And he and eventually as the first chair of theo - ditional teaching for inorganic from taught that wonderfully. Although he retical chemistry in the country. Professor Emeléus or Dr Palmer (there used mathematics, even I, who had By 1957-58, the advanced courses was a choice again). It really was extra - Lab 122 as Tony none, was able to follow what he was for research students were already being ordinarily dull, I have to say, with end - Kirby remembers doing and to be impressed by it. He was taught in Lensfield Road. They had less information on the chemistry of it – spot the a spectacular lecturer who strode up started to move into the new building boron and all the other elements they lecture theatre and down in front of the class – just from 1956, and the change in the facil - taught us about. being built outside what you’re not supposed to do – but ities was dramatic. The photo of lab But then there was another revela - the window people were riveted. ­ 122, where I worked in the 1960s, is particularly interesting – you can see the construction of the roof of the lec - ture theatre going on outside. We remember it going up very clearly – a very interesting thing to be going on outside your window!

Ian Fleming on the people I first stepped into the building in 1956, when it was still a construction site. Parts of it were complete, however, and I went through the door to find my supervisor, the sole reason I had to step into the building. David Cohen was working in room 122, and I went there to make arrange - ments for supervisions, so I saw the building in that state. It was a period of very great change, not only with the new building but also with new ways of teaching chemistry. In our first year, we had a choice of

Chem@Cam Spring 2009 11 History

­ We then moved on to what was So I got the NMR spectrum and, of called the advanced half subject, in course, I couldn’t make head nor tail of which we did more chemistry than had it. Compared to modern spectra it’s ter - previously been included in the second rible – there’s no scale, and the big year. And we had two more lecturers - peaks were internal standards, but it Peter Sykes, who actually talked about came with a very interesting note electrons in organic chemistry, showing pinned to it, saying that there was an us how reactions worked, and Alfie ethyl group in my compound. From Maddock, who showed us that inor - then on I realised that I had to learn ganic chemistry was actually very inter - about NMR. esting. These were remarkable people The most dramatic illustration for me who gave us a new view of the subject, of the power of NMR came 18 months and for that reason I went on with later, when Yusuf Hamied was giving a chemistry; without the influence of lecture on his research into the aphid Sharp, Longuet-Higgins, Sykes and pigments. As I remember it, he pre - Maddock, I would probably have cho - sented a story in which he was trying to sen biochemistry instead! show that the aphid pigments featured In the third year, we were taught by two hydrogens on quinone rings, for Alex Todd, who gave us a really first which there was a chemical test. It was hand account of natural product chem - a beautiful lecture, and well performed istry, the subject he was most interested chemistry that convinced us that the in; by John Harley-Mason, who was a structure he was looking at had two modern chemist, in a rather idiosyn - hydrogens like that. cratic way; and by Malcolm Clark, who But at the end of the lecture, Norman was the single most important individ - Sheppard got up from the back and ual in my student career as he showed said, ‘Yusuf, that was a wonderful lec - us we could go on thinking about ture and beautiful work, but you’ve got chemistry way beyond what had already the structure wrong – I’ve taken the been revealed to us. NMR spectrum of the starting material There was also FG Mann, another tra - and the product, and there is no doubt ditional chemist. While he was a very that there’s only one H on the ring.’ clear lecturer, he simply spoke about froze, and for about a month we could Top: Saunders, It didn’t take long for someone, prob - substrates and products, with no mech - walk on the river. Christopher Longuet- Kipping, Sharpe, ably Malcolm, to show that there was a anisms. For example, he taught a whole Higgins went skating on the Cam, and Emeléus, Palmer, viable pathway. The lesson we learned section on benzpyrimidines, which one day as he was heading out of the Longuet-Higgins was that the chemical test was not reli - would not be taught like that today, as building to go skating, Todd was com - and Sykes; able, whereas NMR was reliable! we teach the generalities of how to ing in and said, ‘What are you doing? Above: the Very shortly afterwards, Dudley think about molecules like this, not You’ll break a leg!’ And half an hour frozen Cam Williams came to Cambridge to give us specifically about individual structures. later, he was in Addenbrookes. Todd had greater strength in NMR and to intro - When we started our PhDs in 1959, great predictive powers! duce us to mass spectrometry, and over there were four women in the whole of Another major change that was tak - the years they seem to answer almost organic as judged by the photograph – ing place at that time was the introduc - everything in the way of structure which was pretty typical of those days. tion of NMR. As an undergraduate, our determination! What a great privilege it What a difference it is today. The other lectures from Delia Agar on NMR were was to live through that period of dra - thing is nearly everybody in the photo - entirely about the physics of the tech - matic change. graph has a jacket and tie. nique – there was no way we would The great thing about this university learn how to interpret an NMR spec - has been the fact that we’ve had first trum from them. Reproduced by class colleagues with whom to talk So it was a great surprise to me dur - permission of about chemistry. It was Malcolm Clark ing my first term of research in 1959 who got me, Tony Kirby and Stuart when Harley-Mason said to me, when I Chem@Cam. Warren going – we all shared Malcolm was puzzling over an unexpected prod - as a major input, and it was his way of uct, why don’t you run an NMR? I © Department of thinking that infected us. asked him what it would tell me, and Below: Maddock, Chemistry, University The year 1962-63 was an extraordi - his response was that he didn’t know Todd, Harley-Mason, nary year - it was the year the Cam but it was a good idea! Clark and Mann of Cambridge and individual contributors.

12 Chem@Cam Spring 2009 www.ch.cam.ac.uk Tim’s beach wedding Technician Tim Layt got married in February – and went all the way to New Zealand to do the deed. His bride Kirsten Scholefield – who used to work in reception here in the department – is a Kiwi, so they went back to her roots for the wedding. It was a bit of a British invasion – 26 friends and family made the trip to make sure Tim didn’t change his mind. When they got engaged a couple of years back, Tim was adamant that it was going to be at least three years before they got married. But that didn’t quite happen. ‘It developed its own inertia,’ he says. ‘People kept asking when the wed - ding was, and it was easier to say that we had a date…’ The ceremony was held on a beach at Scott’s Landing, near Kirsten’s home town of Warkworth in the north island. Despite the torrential rain, the wedding went brilliantly, and everyone had a fab time. ‘It was the most torrential rain I’ve ever seen, and it was really funny watch - ing guests running across the beach with umbrellas!’ Tim says. They were in New Zealand for three A couple of issues ago we published a photo of tree surgeons weeks in total, and had a pre-honey - check out on Friday instead, and spend at work in the car park. This prompted retired department moon there during which time Tim did Friday night and Saturday on the resort’s photographer Eric Smith to send us this photo he took way back his first sky-dive, from 15,000 feet. 100 foot fully-catered five-star yacht in 1959, when health & safety regulations aren’t quite what they Kirsten was gutted she couldn’t jump instead. It was a wonderful surprise are today. Not a job for the faint-hearted, or those with vertigo! too as she had a bad back! ending to our honeymoon.’ The honeymoon proper was a week After a whole month off, it’s a bit of a Comings & goings of unashamed luxury in the Maldives. shock to the system being back in New Staff Susan Smith ‘We were due to fly back at 2.30am on Cambridge. ‘Married life is lovely,’ he Pawel Paczesny Martin McLean Sunday morning so we wanted a late claims. ‘Though we have spent most of Christine (Tina) Jost Leaving check-out,’ Tim says. ‘But unfortunately it so far in five-star luxury! And I’m Asha Boodhun Judith O'Connor Antonia Maria Moya they were full on the Saturday so it was - really enjoying asking people if they’ve n’t possible. Instead, they suggested we met my wife.’ Snow bride Monika

Monika Czifersky, a postdoc in Oren for the wedding, Andreas had his inter - Scherman’s group, got married at the end view, then took the evening plane back of March in the Austrian snow. They’re to Salzburg, and arrived after midnight both from Vienna and love the snow, so it in Vienna. ‘We were very lucky that was the perfect weather for them! everything worked smoothly with the However, there was plenty of poten - flights!’ she says. tial for disaster as the logistics of where The wedding day was sunny and cold, they both were just before the wedding and they held the reception in a mountain were somewhat chaotic. ‘Andreas is still hut just outside Vienna, about 1000m living in Vienna, but he had a job inter - above sea level. ‘We had much more snow view at the British Antarctic Survey in than we expected, but everything went Cambridge the day before the wedding!’ really well. We both love to be in the she explains. mountains, we love snow and skiing, ‘We were getting married in Vienna on hearty soup, snowball fights, and so on. the Friday, so I left Cambridge in the after - So we tried to include as many of these noon of the Wednesday, and met Andreas things as possible into our wedding. near the airport in Linz to give him my Everyone had a great time, and it was an house keys and car keys so he could pick unforgettable day for the two of us.’ up the car I’d left at Stansted. I then had to They followed the wedding with a drive to Vienna, while he took the evening week’s honeymoon in the Swiss Alps, plane from Salzburg to Stansted.’ again with lots of snow. And they also On the Thursday while Monika was had a bonus wedding present – Andreas busy with the last minute arrangements got the job!

Chem@Cam Spring 2009 13 Chat lines Fancy a drink?

Nathan Pitt was on hand with his camera to catch some of the faces old and new at last December’s staff Christmas party

Left: Alan Battersby and Dick Barton; right top: Sue Johnson and Mike Todd-Jones; right: Tim Dickens and Peter Murray-Rust; right below: Julie Lee and William Prist

Above: David Gillingham and Mike Sleep; above right: John Holman and Sue Harding; right: David Woollard and Ken Veal

Left: Liz Alan, Anne Railton, David Watson and Christine Wilson; above: High fives for Sian Bunnage and Pat Chapman

14 Chem@Cam Spring 2009 Puzzle corner Last issue’s winners ChemDoku gets personal… ChemDoku Another fine response to the ChemDoku puzzle, most with Mt Rf correct answers, plus an honourable mention for Donald Stedman and his wife Hazel, née Cooke, who believed there was a misprint and suggested a change to the puzzle. Md Sg Rg However, the following all got the correct answer, so hope - fully the original version was solvable – either that or every - Fm Rf one else got it wrong. And correct answers were received from Bill Collier, AJ Wilkinson (who says, is it me – I am 80 – or are your puzzles Es Rg Mt Sg getting harder? This is the first I have solved for a year or so and I have the impression it was the hardest Sudoku I have Sg Cm ever completed), Jim Dunn, Helen Stokes (who claims ChemDokus are very good fun), Reg Lewis (who says he’s Md Fm Rf Sg from the infamous 1946 class), L Smithurst, CW Haigh, Nick Broughton, Ian Fletcher, John Wilkins, Pat Lamont Smith, Annette Quartly, Julian Langston, Karl Railton-Woodcock, Rg Rf Richard Chambers, Bruce Sargent, Robin Cork, Chris Shorrock, Joanne Castle, John Billingsley, Christian Hill, Roger Cm Bh Mt Duffett, Tom Banfield, David Wilson, Mark Alderton, Raymond Holland, Norman Sansom, Richard Brown, Alison Griffin and Godfrey Chinchen. And the winner is... as chosen by this Sg Cm issue’s glamorous assistant (actually my lovely hubby being a random number generator at the end of the phone line)... The return of ChemDoku garnered its usual large crop of Norman Sansom. Congratulations! entries, so it would seem rude not to provide our loyal read - ers with another chance to show off their powers of deduc - tion without the benefit of numbers in the grid. Chemical crossword This time, we’ve replaced said numbers with nine chemical elements named after people – which, of course, means that 12345 some of them barely exist, and certainly don’t exist in nature. WSCo Ne Ca SUAl Meitnerium, for example, was discovered when a single atom 67 8 was created by bombarding a target of bismuth-209 with Se ICHe C Eu Ta N accelerated nuclei of iron-58. 9 10 11 12 All you have to do is to arrange the chemical symbols of the Te S La Er K Cl Co Re nine different precious metals in the grid so that each appears 13 14 15 16 once – and once only – in each horizontal row, vertical col - N Er YS CYPr US umn and 3x3 square. Easy! 17 18 19 Ta Mo ON S Sm O Th Er

20 21 22 W Re NOVINe V Benzene resistance 23 24 25 26 P Ar Ar Se NI C CAt And finally for this issue... a part-chemistry, part-physics puz - zle from Graham Quartly. He says that while the problem is 27 28 29 INCa C Sc H Ar I based on the structure of benzene, he had been trying to couch it in terms of buckminsterfullerene – but the maths got 30 31 32 33 Xe Re CO V Er As BO a bit excessive for that! And the puzzle is... The trusty chemistry technician at 34 35 36 La SUNd I Al SIN St Anne’s was called upon to supply a model of benzene at

37 38 short notice. As the usual set of atoms and bonds were at Te NS Es Ce Al O Ne home for the apple- weighing problem Graham Quartly’s latest crossword provided another good from a couple of influx of entries, without too many complaints about the £20 prizes are issues ago, she Spanish word and the dance move, although one correspon - on offer for plundered a bag of dent thought the latter was most unfair as he is a confirmed each puzzle. 99 ohm resistors Strictly Come Dancing avoider! And I think the sports channel Send entries from the physics ‘Setanta’ caused a little confusion... by email to department, and Anyway. Correct solutions came from Bill Collier, Jim Dunn, [email protected] hastily soldered 15 L Smithurst, Ian Fletcher, John Wilkins (Fiendish!), Pat or by snail mail of them together to Lamont Smith, Ian Potts, Julian Langston, Donald Stedman, to Chem@Cam, make the familiar Karl Railton-Woodcock (who reports that as the UK froze, the Department of hexagonal star, with temperature in Melbourne hit 45.4°C), Robin Cork (who says Chemistry, parallel resistors to the crossword was a big challenge – congratulations to the University of indicate the alter - setter!), John Billingsley (who commented that it’s really nice Cambridge, nate double bonds. to come across new words), Keith Preston, David Stewart, Lensfield Road, What is the effective Roger Duffett, David Wilson, Norman Sansom, John Nixon, Cambridge resistance between Raymond Holland, Richard Brown and Nicola Farrer. And my CB2 1EW diametrically oppo - husbandly random number generator picked John Wilkins as site hydrogen atoms? the winner.

Chem@Cam Spring 2009 15 Never mind the health scares, Grandma – you know pumpkin soup needs salt!

Chem@Cam is written, edited and produced

by S ARAH H OULTON

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