Chemical of the Week 19 -EDTA

I

image

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.

image.png

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.

Advertisements

Why Study Chemistry ?

 

image

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.

image

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.

image
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

 

Waiting for a Bus !

It’s a bit like buses, you wait for ages then four come by at once. Of course the big news story this week is the positive identification of four new elements 113, 115, 117 and 118. (For those of you a long time out of the classroom this number is the atomic number which is the number of protons found in the nucleus). The actual names for these elements are up for discussion with debates over whether they should be after people, countries, minerals or places to name a few suggestions. There have been lots of articles about these elements, a great graphic by compound interest and an excellent blog post by Dr Eric Scerri.

http://blog.oup.com/2016/01/four-new-super-heavy-chemical-elements/

It popped up as a question on the BBC quiz show Pointless and I even spotted a petition on Twitter to name element 117 octarine in honour of Terry Practchett. Oh and my favourite -naming one after Lemmy, the bassist of the heavy metal band Motörhead.

image

But what I want to talk about is the island of stability. In nuclear physics, the island of stability is the prediction that a set of heavy isotopes with a near magic number of protons and neutrons will temporarily reverse the trend of decreasing stability in elements heavier than uranium. Now magic is not something that you usually hear scientists talk about but it refers to the numbers of protons and neutrons that give stable atoms. It goes against everything we’ve been taught in that as nuclei get bigger they get more unstable, and that any element greater than uranium in the Periodic Table does not occur naturally. So where do we find this island and why an island ? If you look at the graphic above which is the relationship between nucleons and stability and use a bit of blue shading it becomes clearer. The island of stability is a region of the periodic table where elements’ half-lives increase after a large group of elements with very short decay times. This is were we find the super heavy elements who have atomic numbers greater than or equal to 112. The discovery of element 114 back in 1998 was the beginning of the this quest for the island of stability. And why are some of these super heavy elements stable – I think I’ll leave that to the nuclear physicists to explain.

Making these super heavy elements is no mean feat and there are only certain places in the world with the capabilities to do so including the RIKEN Institute in Japan, Joint Institute for Nuclear Research in Russia, and Lawrence Livermore and Oak Ridge national laboratories in the U.S. These elements have been reported in the literature for quite a while now with first experiments on 113 and 115 starting in 2003. To create these elements researchers smash smaller elements together. For instance, to make element 117, calcium nuclei (20 protons) were smashed into a target of berkelium (97 protons). Interestingly they never actually recorded the new element itself but evidence of its decay products. Why bother spending so much time making these elements that really do not have any everyday uses – it’s that old science chestnut, we add to the bank of scientific knowledge and we learn a bit more about atomic structure. As some may have longer half lives we may be actually able to do experiments with them and one day who knows where that could lead !

Fancy a job on the International Space Station ?

One of last years most fascinating tv programmes was the Horizon special on the ESA astronaut Tim Peake. Even though chemistry is my thing space continues to fascinate and inspire me. Whether it’s the Mars rover or the disappearance of the ESA Beagle I always try and mention newsworthy space stories in a lesson. There is an excellent YouTube clip from NASA about the scientific machinery on board Curiosity, including a mass spectrometer, and I find it an excellent introduction to Mass spectroscopy at AS level. Recently I blogged about growing crystals and believe it or not this is one of the tasks of an astronaut during their time on the International Space Station.

Growing crystals in microgravity has long been a focus of space science. I can remember the Saturday night clearly in 2003 when news broke that the space shuttle Columbia had exploded on its re-entry into Earth’s atmosphere. At the time I was completing my teacher training and also working part time as an editorial assistant for the American Chemical Society journal ‘Crystal Growth and Design’ (working for a peer reviewed journal is totally a post all on its own). So as the news filtered through and I began to understand what Columbia’s scientific mission had been about, the enormity of the tragedy resonated with me. The Columbia Space shuttle was on a mission to complete lots of science in microgravity. This included growing crystals, combustion studies and the development of stronger, more resilient metals and alloys. The Columbia space shuttle was essentially a science lab in space and the seven brave astronauts were trail blazers for the scientific community.

 

image.jpeg

So why grow crystals in space? Space grown crystals are of greater purity than those grown on Earth and have more highly ordered structures which significantly improves their X-ray analysis. There has been a focus on growing protein crystals in space. Protein structural information plays a key role in understanding biological interactions. Scientists discover new drugs now by understanding the orientation and connectivity of the atoms within a molecule and how this drives its interaction with atoms in another molecule (for example an enzyme that might be able to be ‘switched off’). This allows for the development of new pharmaceutical treatments for both chronic and acute illnesses such as lymphoma , psoriasis, rheumatoid arthritis, AIDS and influenza to name but a few. The International Space Station provides an opportunity to have a complete crystallographic capability which was previously not possible with the space shuttles.  The role of the astronaut is changing – the Space agencies need astronauts who understand the science. There are amazing opportunities for our next generation of scientists to be groundbreaking – not on Earth but in Space – helping to cure the illnesses that blight us humans.

 

p.s. Here is a good activity for growing crystals from NASA

http://www.nasa.gov/pdf/675572main_Science%20Activity-SOS.pdf

 

Chemical of the Week 18 -Atropine

image.png

This is a quick post about a chemical that saved one of my favourite characters on TV last weekend. It was a syringe of the chemical atropine administered fortuitously to Quinn before his exposure to sarin gas that meant he lived to tell the tale ! Atropine, or (RS)-(8-Methyl-8-azabicyclo[3.2.1]oct-3-yl) 3-hydroxy-2-phenylpropanoate as it is systematically known as, is a compound found in the deadly nightshade plant. Isolated from the plant back in 1833, it now has a variety of medical uses including in the treatment of Parkinson’s disease, maintaining regular heart function during surgery and even treating scorpion stings. There is a really interesting article about the synthesis of atropine in the link below. Richard Willstätter completed the synthesis in 1901, and it demonstrates the challenges faced by the organic chemists of that era who had to identify their product by carrying out chemical tests and comparing to the natural product rather than analysis using spectroscopic techniques available today.

image.jpeg

 

So how did this molecule save Quinn ? Sarin is an organophosphate nerve agent. It acts by inhibiting the enzyme acetylcholinesterase. Acetylcholine is a neurotransmitter activating nerve fibres that cause muscles to contract. Sarin forms a covalent bond with a residue at the active site on the enzyme making it unable to bind to acetylcholine. This means the acetylcholine molecule is not broken down after it activates the fibres, the delicate balance of acetylcholine and its degradation products is disrupted, and acetylcholine builds up and continues to make the nerves connect over and over and over again. How does atropine work ? It blocks the acetylcholine receptor stopping it from working in the first place. This is not ideal as it means that the nerves are not driving muscle function but it stops seizures and convulsions.

So thanks to atropine I can sit down tomorrow night to another instalment of Homeland knowing that one of the CIAs most prolific spies is back in action and may still save the day !

http://www.chm.bris.ac.uk/motm/atropine/synthesis.htm

COP21 – What’s your view ?

image

At the minute the United Nations conference on climate change is finishing up in Paris. It is being referred to as COP21 as it is the twenty-first session of the Conference of the Parties to the UN Framework Convention on Climate Change. Probably the most famous conference was the Kyoto summit in 1997 which resulted in the Kyoto Protocol, a legally-binding deal that now appears on our AS specification. The protocol was based on the premise that both global warming exists and man-made carbon dioxide emissions have caused it. As well as carbon dioxide they focused on the following greenhouse gases; methane, nitrous oxide and sulphur hexafluoride and also two groups of gases, the hydrofluorocarbons and perfluorocarbons.

So where are we now, nearly 20 years later ? The protocol itself did not come into force until 2005 with the aim that industrialised countries would reduce their collective emissions of greenhouse gases by 5.2% compared to 1990. Of course the most important footnote is that the US did not sign up and it seems that now the Kyoto protocol is considered a failure as although certain countries met their targets any benefits were wiped out as large industrial nations such as the US and China continued to pollute unabated.

Now, being a scientist encourages a pragmatic approach with clear presentation of all the data. But I can’t help but feel the politicians’ hearts are not in it when reading about the European Union Emissions Trading System. The name explains the system where energy companies become regulated and allowances set. They can trade their allowances which provides them with an incentive to reduce their emissions. The system seems to have modest gains as they gave very generous initial caps and developed an offsetting process if the companies invested in technologies in the developing world.

However, is this the right approach? Surely the focus should be driving new green technologies or older technologies such as nuclear and the part they play in reducing greenhouse gas emissions? At the minute green chemistry seems like a ‘strand’ of chemistry, a topic on an examination specification, and not an integral part of both pupils and the general public’s scientific understanding. Unfortunately, the COP21 roadshow will move on and the world leaders’ focus will turn away from environmental concerns. But what can we do ? There are many levels we can work at from daily tasks such as recycling or being energy efficient to encouraging our pupils to consider STEM pathways. We need to continue to focus our efforts on getting them to consider careers in science, using their ability and skills to design and engineer solutions instead of avoiding the issues and leaving the problem to the next generation.