Chemical of the Week 18 -Atropine


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.



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 !


COP21 – What’s your view ?


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.

It’s Crystal Clear !



I have decided to write a post about my most successful pupil crowd pleaser – no not potassium and water, it’s over too quickly. Growing crystals has become my go to project to reel in the budding chemists. It really is a magical experience although the fiddily process of looping the seed crystal is painful for my clumsy spade like hands. However hand a seed crystal over to the pupils and in no time they’ve set up and are taking the first of many pictures over the coming days and weeks. This is where mobile devices come into their own, pupils can take daily pictures of the crystals and look at how they grow over a period of time. Last year we really focused on crystal growing as it was the international year of crystallography. The International Union of Crystallography ran a world wide crystal growing competition and it was also the focus of the RSC global experiment. This synchronised approach by both the RSC and IYCr allowed us to focus on crystal growing withdifferent year groups and abilities with varying success but definitely enthusiasm and fun!

Patterns are all around us, look at a tiled roof, wall paper and even wind ripples in sand. The repetitive nature of a pattern is repeated at atomic level in crystals. Crystals are solids composed of atoms, ions, or molecules arranged in a pattern that is periodic in three dimensions. Crystallography is the science of determining the arrangement of the atoms in a crystalline structure by studying diffraction patterns when x ray’s interact with each atoms electron cloud. Nearly every solid can crystallise which means that theoretically we can obtain ‘a picture’ of the arrangement of atoms in a substance. However, I remember the rows of beakers littering PhD students desks (as they tried different solvents and different evaporating times)and the dejected look on their faces as they returned from the crystallographers room – growing suitable crystals is an art in itself !

It was William Bragg who allowed us to investigate crystals. Bragg’s law on the diffraction of X-rays by crystals makes it possible to calculate the positions of the atoms within a crystal from the way in which the X-ray beam is diffracted. The technique of crystallography has underpinned some of the best science of the last century. It has paved the way for the elucidation of the structures of many biological molecules with the most notable being Watson and Cricks structure of the DNA double helix, with those preliminary experiments carried out by Rosalind Franklin. Crystallography provides essential information in so many scientific fields such as materials science, medicinal chemistry and geology to name a few. And science likes to reward those crystallographic discoveries – check out the link below to see the crystallography based Nobel prizes. Only two years ago Dan Shechtman was awarded the prize for his work on quasicrystals which are crystalline structures that break their periodicity. Normal crystal structures can be described by one of 230 space groups, which describe the rotational and translational symmetry present in the structure. Shechtman rapidly cooled an alloy of aluminum and manganese and found that it showed the forbidden five fold symmetry. He had to fight the established scientific beliefs about crystals to establish this new field and I love that he apparently said when analysing his crystallographic data – “There can be no such creature.”



Check out the Guinness Book of Records attempt at building a replica of crystalline sodium chloride. It’s 3m tall and has nearly 40,000 balls ( representing the sodium and chloride ions) and nearly 12km of sticks. The real beauty of the lattice is that it gives us a visual representation of what’s really in a crystal of salt, allowing us to the bask in the order and symmetry of our chemical world !