Brexit

It’s twenty years since I was part of a multicultural, multinational chemistry research group at Queens University Belfast, a rare thing in Northern Ireland in the days before the Good Friday Agreement. All credit to my supervisor who took students and post docs from far and wide to provide me with the educational experience that I dream of for the students I teach today. Science has now become somewhat of a focus for Northern Ireland’s beleaguered post conflict economy – and it felt that the experience I had as a PhD student was beginning to be replicated in NI start-up scientific based companies funded in part by the EU. So how will the recent referendum decision to leave Europe effect the choice of the next generation and in particular those wishing to study science ? There is a link below to the statement released by the EPSRC in regards to the referendum decision.

There is so much that can be said and so many people with much more experience (and much more to lose) than me but here’s my initial thoughts – My major worry when reading this is both the uncertainty and the timeframe – any teacher will recognise 2 years as that crucial time for choices to be made – whether it be GCSEs, A levels or even getting to that final year of a degree. Will this enough to put some of our young people off studying science ? Many young people with science qualifications in the UK are keen to move around Europe (and beyond) gaining skills to allow them to return closer to home as their career progresses. The flip side is that many science based companies recruit around Europe for scientists to bring their skills and technical knowledge to the UK. Not being part of the EU (or in the process of leaving) brings a degree of uncertainty in particular about funding as access to EU Horizon 2020 grant system may change. The movement of scientific talent had already become an issue before the referendum when the earning threshold for non-EU immigrants was being set at £35,000. This threshold has major implications within the younger scientific community, for example scientists obtaining their first post degree job or post doctoral position.

My other concern goes back to my days in a research group. There was a massive amount of administration behind the scenes to allow funding such an international mix of students and post doctoral researchers. Surely leaving the EU can not make this task any easier. Most research groups do not work in isolation, a quick check of publications shows that a lot of research papers are written by more than one contributing group. Will we still have the same academic collaboration between British research groups and those in the EU? I have no doubt that it will not be the groups themselves that will prevent this but rather the funding bodies and the extensive paperwork which will slow down collaborative processes. There have been a wealth of articles about the implications of the referendum on science, a few of which I’ll link below and leave you with an excellent quote from the current President of the Royal Society Professor Venki Ramakrishnan – ‘Many of the global challenges we face can only be tackled by countries working together’.

http://www.rcuk.ac.uk/media/news/160706/
http://www.rsc.org/chemistryworld/2016/07/explainer-what-will-brexit-mean-science
https://www.theguardian.com/education/2016/jul/16/research-funding-hit-by-brexit-vote

Connectivity Rules !

So with my pupils having just finished their final organic paper I decided to base this post around connectivity – the attachment of atoms in a molecule. I introduce its importance in class by showing this brilliant video by Professor Dave which he made after spotting a poor structural representation of a molecule in the opening credits of Brian Cox’s tv programme. This video emphasises the importance of correct representations and after that I show no mercy and the red pen is out ready to start circling ! Mark schemes also see connectivity as an important chemical skill and you can see that when drawing an alcohol the examiners will penalise if the connectivity of the carbon to oxygen is not shown correctly.

Only last week I read a post by the eminent chemistry blogger Derek Lowe about a structure he spotted in a paper about piperazines.  Now, although the connectivity is correct he points out the poor bond lengths and angles. Even more disappointing they do not show the stereochemistry of the hydroxy groups and that could mean the diagram could represent up to 8 different structures. I would like to think by the time our A level students sit their final organic paper they understand the importance of correct representation and if a career in chemistry beckons they would not let mistakes like this occur.

So outside of chemistry who really cares? Well this is a true story. Recently I was in a very trendy coffee shop with the organic chemist (check out his guest post for me here) who noticed that the barista had tattoos of the structures of caffeine and theobromine (chocolate). When the organic chemist mentioned the tattoos the barista became quiet and sullen. Turns out she thought he had spotted the mistake on the structure of caffeine, a methyl group CH3 was incorrectly tattooed as OH3. A permanent reminder that there is no room for mistakes with your structural representations.

An Element that’s stood the test of time !

This is my fiftieth post and I have been mulling over what to make it about – it’s my half century celebration and I never thought I would have kept the blog going so long. So with all the talk this week of naming the new elements I thought I’d go back in time to element number 50 and boy has it been around for a while ! It’s TIN – named for the Etruscan God Tinia and its symbol Sn ( always a good quiz element ) from the Latin stannum.

 

One of my favourite books is ‘Napoleons Buttons – 17 molecules that changed history” by Penny le Couteur. Unfortunately I lent it out to a pupil in school and it wasn’t returned, and now it can only be bought on Amazon for an extortionate price ! It told the story of Napoleon’s retreat from Moscow and how in the depth of winter the buttons on his men’s uniforms started to fall off. Apparently they were made of tin and when the temperature dropped it changed from the allotrope shiny beta tin to brittle alpha tin (apparently the transition temperature is 13 oC but small amounts of antimony or bismuth can prevent this happening). This campaign was seen as the turning point in the Napoleonic wars and if the hypothermia suffered by Napoleon’s troops had been avoided would European history have played out differently ?

 

But tin goes back much further than the 1800’s and was known to ancient civilisations. Tin does not occur as a native element but can be isolated by heating it’s ore in the presence of carbon. Tin melts at a relatively low temperature (230 oC) so it has been used widely in alloys in particular bronze. Bronze is a mixture of about 80% copper and 20% tin ( the composition changes depending on the type of bronze required). The Bronze Age started about 3000 BC ( linking the Stone Age with the Iron Age) and the combination of stone and bronze allowed for tools and weapons to be made. The earliest tin-alloy bronzes date to 4000BC in Iran and Iraq and as copper and tin mines are not found together it involved a lot of trade to make bronze. Bronze is hardwearing and there is no superficial oxidation due to a barrier of copper oxide. However, it soon was superseded by iron as although not as durable it was more accessible. Nowadays bronze is the reserve of church bells and medals but once upon a time it defined an era.

So forget the tinfoil, tin soldiers and even the tin man  -this element deserves its accolades, it’s time for tin to take its place as a defining element of the Periodic table, a history shaper and game changer.

Lend me a fiver !

So chemistry made the front of The Sunday Times – as it was big news that the five pound note is changing from paper to polymer.  The polymer in particular is biaxailly oriented polypropylene (BOPP) and the great thing about it is any GCSE student could draw its structure ( the biaxially oriented refers to a method of extrusion during production).  The old A level syllabus went further and looked at the different types of polymer formed, both crystalline (isotactic and synotactic) and amorphous (atactic), due to the presence of stereocentres.  Polypropene (polypropylene) is an addition polymer and is produced using a Ziegler-Natta catalyst ( titanium chloride with a co catalyst of triethylaluminium). Karl Ziegler and Guilio Natta were awarded the 1963 Nobel prize for their contribution to polymer chemistry.  

 

The Bank of England claim that polymer banknotes are harder to counterfeit, more durable and cleaner than paper banknotes. But not everyone is happy about this change – apparently the notes are 15% smaller and there may be issues with ATM machines, some estimating the change may cost up to £236 million. But my concern, what about burning  the money – if we change from paper to polymer will the alcohol/water just run off not allowing for that good old chemistry party trick !

http://www.stevespanglerscience.com/lab/experiments/burning-money/

Famous Chemists – Fritz Haber

The Haber process – well where do I start – it’s probably the most important industrial process of the last century and I could list what the syllabus requires us to impart to our students, that’ll be equations (don’t forget reversible arrows), conditions, uses of ammonia ….. but really how are we ever going to convert the masses when you literally watch them fall asleep before your eyes – so what’s a chemistry teacher to do?

Open the classroom door and bring in Fritz Haber – the man who got the Nobel prize in 1918 for the process. But hold on, why is there only fleeting acknowledgement to him on the Nobel website? Well, that’s because Fritz Haber was a very complicated individual. We’d like to think that Fritz spent his life pondering the importance of fixing nitrogen to allow us to grow more crops and feed the growing population, but no – Haber was too busy developing chemical weapons in WW1 including the use of the chemicals chlorine and bromine. After the war he tried to raise funds to pay off the German reparation payments by unsuccessfully attempting to extract gold from seawater.

Haber was a patriotic German, to the extent that his wife Clara’s opposition to his research into chemical weapons and her subsequent suicide did not sway his views. However, Fritz Haber was also a Jew and this began to play an important part in his destiny with the rise of Nazism in the 1930’s. Haber’s self confidence and ambition began to falter as he was singled out for his Jewish heritage. He had to leave Germany and was able to secure a post at Cambridge university but here he was given the cold shoulder by other eminent scientists unhappy with his role in Germany in WW1. Now it all could have ended there with Haber heading off to a research institute in Palestine where he passed away quietly en route in 1934. However, Fritz Haber’s legacy chillingly did not to end with his death. It turns out that some of the research he had carried out earlier in his career was developed by the Nazis to produce the deadly gas Zyklon B which was to be used in the gas chambers. It is thought that some of Haber’s relatives died in the concentration camps- possibly in gas chambers.

This is one of the posts that I had thought about when I initially decided to blog but I have put it on the back burner for a while. Why? Well, the story of Fritz Haber made me think of the role of scientists in today’s society and especially if in a country at war or considering it. Was Fritz Haber’s ambition and patriotism so unusual and are all scientists morally upstanding ? What happens if you pick the wrong side, are you consigned to a damning legacy ? I still don’t know the answer and maybe Fritz Haber’s legacy is that he makes scientists feel uncomfortable.

The Name is Bond – Hydrogen Bond !

Well, what’s a hydrogen bond I hear you ask – who cares is probably what most people are secretly muttering under their breath. But yet again, it’s a fundamental chemical phenomenon that allows life on Earth as we know it – no hydrogen bonds, no liquid water, need I go on! Firstly let’s look at the definition and diagram of a hydrogen bond – a hydrogen bond is the electrostatic attraction between polar groups that occurs when a hydrogen (H) atom bound to a highly electronegative atom such as nitrogen (N), oxygen (O) or fluorine (F) experiences attraction to some other nearby highly electronegative atom.

Nowadays it seems like an obvious phenomenon when we look at the higher than predicted boiling points for certain hydrides but the acceptance of their presence seems to have been a slow process for the chemical community. Initial investigations seem to have taken place in the Lewis (that’s G N Lewis who defined an acid as an electron pair acceptor) research group and first publication by Latimer and Rodebush dates back to 1920. Of interest it was believed that Lewis had tried to encourage the scientists in his team to take the section on this hydrogen bond out of the paper before publication. I found an excellent paper about the history of the acceptance of the term hydrogen bond which ran for over twenty years and have put the link below. By the end of the 1930’s Linus Pauling mentioned the hydrogen bond in his seminal book ‘The Nature of the Chemical Bond’ and so began the journey identifying hydrogen bonds as the important interactions that give us the three dimensional biological molecules that are the building blocks of life.

History of Hydrogen Bond
Proof that these bonds exist has been confirmed by crystallographic studies and it was Pauling who was at the forefront of this work. Crystallography uses x-rays to study the structure of molecules and how atoms are bonded together. In 1948 Pauling was studying the three dimensional structure of proteins and he identified hydrogen bonds as holding the polypeptide chains in an alpha helix. This discovery was considered the dawn of molecular biology and is thought to have contributed to Watson and Crick’s discovery of the structure of DNA.

So where do we find hydrogen bonds? DNA, proteins, water, ethanol, polymers and the list goes on! And this week an entirely new class of hydrogen bond that forms between a boron–hydrogen group and the aromatic, π-electron system of a benzene ring has been reported. Interestingly this work has been completed by both theoretical and synthetic chemists and may have applications in boron based drugs. Recent publications show that we are still identifying the presence of traditional hydrogen bonds in molecule interactions and also discovering new types such as that just reported. The humble hydrogen bond is the glue that gives us Nature’s building blocks – it’s much more than just a chemical bond !

Chemical of the Week 20: Chlorophyll

Anyone who has a drive to work knows the frustration of morning travel and wasted time but recently I’ve discovered a way to avoid the boredom – podcasts ! In particular the Radio 4 In Our Time Science series by Melvyn Bragg and it was the photosynthesis programme that got me thinking about chlorophyll. I’ve never really given the chemical process of photosynthesis much thought as it is firmly rooted in the biology curriculum but all that changed last week.

The combination of carbon dioxide and water to make glucose and oxygen is no mean feat and the elegant structure of the chlorophyll molecule allows for the absorption of light to drive the reaction. So what is chlorophyll – it has a porphyrin ring structure attached to a protein backbone. The porphyrin is built up of pyrrole molecules – 5 membered aromatic rings which are made of four carbons and one nitrogen atom. This ring system acts as a polydentate ligand and has a magnesium cation at its centre. It is delocalisation of electrons around this aromatic porphyrin system that allows the absorption of light that kick starts the photosynthetic process allowing the production of the energy-storage and transport molecules ATP and NADPH. Off interest is that chlorophyll absorbs light in the blue and red regions of the electromagnetic spectrum reflecting the mid region hence plants are green! You might also notice the similarities of the structure of haemaglobin and chlorophyll, both having porphyrin ring structures. You can not help but be transfixed by these amazing natural macromolecules which are not easy to make synthetically. A few months ago a guest post centred around the great organic chemist R B Woodward and one of the natural products he made was chlorophyll.

 

So probably the more important question is how do carbon dioxide and water react to produce an organic molecule? It’s obvious that it’s not a straightforward process and something that we don’t see happening without specific conditions. Water is in a sense acting as a fuel adding electrons to the carbon dioxide to allow it to grow into an organic molecule. The podcast mentioned that it might not have been water originally but iron or hydrogen sulfide acting as the electron donors. During this process water is oxidised forming oxygen, hydrogen ions and electrons 2H2O –> 4H+ + O2 + 4e- (photolysis). The conversion of carbon dioxide to glucose can be followed using the Calvin cycle. Carboxylate/oxygenase enzymes catalyse the ‘carbon dioxide fixing’ allowing it to combine with a five-carbon sugar, ribulose1,5-biphosphate. This intermediate quickly breaks down to give molecules with three carbons ( 3-phosphoglyceric acid ) which go on to build glucose.

Now anyone who knows me knows that this foray into biology is not a comfortable one (that’s my disclaimer!). It’s a pity that chlorophyll doesn’t get a mention on the A2 chemistry spec when we are studying polydentate ligand systems – surely this is the ultimate complex without which the World would be a truly different place! Oh and I loved the fact that when the historical biochemist talked about the evolutionary photosynthetic process, oxygen was originally considered a toxic (reactive) product – how things have changed !

Chemical of the Week 19 -EDTA

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At the minute I love that nine o clock feeling, when the marking is done, lunches are made and it’s time to sit down to the box set. So over the last week we have been immersed in the Netflix series ‘Making a Murderer’. Well, surely this must be taking me away from all thoughts of chemistry, but just like Homeland up springs a molecule which plays a leading role in the story. This time ethylenediamine tetraacetic acid which is more commonly referred to as EDTA. It’s IUPAC name is 2,2′,2”,2”’-(Ethane-1,2-diyldinitrilo)tetraacetic acid so EDTA is definitely less of a mouthful. It pops up at the end of the A2 course when we are looking at multi dentate chelating agents.

So what is it doing in a real life court room drama – well there is debate over whether a blood sample was planted at a crime scene and one way to establish did the blood come from a storage vial is to test for the presence of EDTA. EDTA is added to blood as it acts as an anti coagulating agent which means it stops the blood from clotting and is the best chemical for the preservation of cellular components and morphology of blood cells. How does EDTA work ? Well if you look at the structure of the molecule you will see that it has four carboxylic acid groups and two amine groups.  The acid groups can be deprotonated meaning that there are six pair of electrons that can act a ligands around a central metal ion, in the case above being the calcium ions in the blood. In the complex [Ca(EDTA)]2–, chelation involves the two nitrogen atoms and the four deprotonated (-COO–) groups (the overall charge of the complex takes into account these 6 coordinate bonds). EDTA is a very hard working chemical and has uses in the food industry, detergents, water treatment and is even used to treat lead poisoning.

Well back to my tv show – it turns out the test carried out in FBI labs didn’t detect any EDTA but an analytical chemistry expert for the defence offered the observation that as the level of detection for the test was not reported she could not conclude that there had not been any EDTA in the blood sample. I read an interesting post from a chemist who suggested that a control sample should be run. This could be achieved by putting an EDTA blood sample on the car surface and then collecting swabs in the same way as the evidence swabs. As always science does not lie but it is important that it is presented in its entirety.

Why Study Chemistry ?

 

So I always knew it would happen, in the darkest days of the academic year the enthusiasm for blogging would wane. But as always social media through up a nugget to get me thinking again. This time it was a link to an Irish Times article about choosing the right degree course at university.

http://www.irishtimes.com/student-hub/course-decision-cannot-be-taken-lightly-1.2508463

In school I have recently been tidying up our careers notice board and I had contacted some past pupils doing science based courses and got them to write a piece on how studying chemistry helped them. In NI, as we are a small economy, there are only limited science career pathways for young people who want to build their lives here but what stands out from their pieces is their enthusiasm for their subject / chosen career. And that’s what the piece in the Irish Times highlighted – pick a subject or career that you have a passion for not just one that you think will serve you well.

So what jobs do people with chemistry degrees and PhDs end up in – if I look at the class of ( ok I’ll not reveal it but let’s just say we were all looking forward to that great millennium party!) my classmates have ended up in both the public and private sectors. Within the public sector there are teachers (both at secondary and tertiary level) and those in areas such as the Environment agency and Invest NI. In the private sector many got jobs in Ireland’s growing scientific sector, in particular Almac, Norbrook, Randox, Pfizer and BMS to name a few. I know some of the people who read this blog are friends and in particular those who I studied with so I’ll leave the floor open to you – would you advise your younger self to study a science based degree ?

On This Day …….

What’s in water ? Well everyone knows it’s a compound containing hydrogen and oxygen. But of course that was not always the case, in fact water was considered one of the four elements in ancient Greek philosophy. So how did we come to realise that water was a compound and not an element, and how did we learn what it was composed off ? On the RSC ‘On This Day in Chemistry’ website  it reports today that on 15 January 1784, the scientist Henry Cavendish announced the composition of water to the Royal Society.  He presented the results of experiments where he had burned dephlogisticated air (oxygen) and inflammable air ( hydrogen) together observing a dew had formed on the apparatus. The inflammable air was produced by reacting acid with a metal which of course is how we produce hydrogen in our practical classes today. With further experiments he discovered that twice as much hydrogen is required than oxygen.

Cavendish was not alone on working on experiments to produce water, Joseph Priestley had also observed water in experiments (using ordinary air instead of oxygen) and Antonine Lavoisier also claimed to have discovered water. James Watt was Cavendish’s most serious contender for the discovery. Watt, a Scottish engineer, had a passion for steam engines and in his investigations to make them more efficient he also claimed to have discovered the composition of water. Cavendish was seen as a chemist whereas Watt was considered more of an inventor so two camps formed with their supporters and the ‘Water Controversy’ began. Interestingly,  the debate centred around the fact that Watt had established the concept of water as a compound before Cavendish produced the experimental data. Cavendish, who was always slow to publish due to his crippling shyness, eventually won the battle as later studies of his notebooks attributed the discovery to him.

Henry Cavendish Portrait

Cavendish was a complex individual who had great problems with social interaction which some now believe may have been autism. As with scientists of his time Cavendish worked in other fields such as electricity, the density of the Earth and even thermodynamics (James Watt also patented an idea that could be seen as the fore runner to the photocopier and also coined the term ‘horsepower’). At that time there was not the clear division between physics and chemistry that is seen today – a relative later donated funds for the Cavendish laboratories at Cambridge university. These are found in the Physics department and are probably one of the most famous sets of labs in the world producing a host of Nobel prize winners including Thompson, Rutherford, Watson and Crick to name a few. Because Cavendish was concerned with science for understanding not for profit at the time he was considered a ‘gentleman of science’ and I think that is a fitting tribute