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Oxygen

Oxygen is a radical, a rebel, an emotionally unstable element with a crazed look in its eye. Oxygen, named by Antoine Lavoisier after the Greek ‘begatter of acids’ in the mistaken belief it was a component of all acids, is part of the Chalcogen family (group 16 in the periodic table). The whole Chalcogen family is a bit odd from top (oxygen) to bottom (polonium) but oxygen is unhinged in a way that makes all the others slowly shake their heads in disbelief. Oxygen was independently discovered by Joseph Priestly (theologian, legendary chemist and staunch defender of the phlogiston theory) and Carl Wilhelm Scheele (indirect poisoner of thousands through the arsenic-based pigment ‘Scheele’s Green’ used in wallpaper, toys and clothes throughout 18th century Europe, his habit of sniffing and tasting any new compound contributed to his early death).

Without oxygen nothing burns

Oxygen is the third most abundant element in the universe, the most abundant element on Earth by weight and the largest proportion of our bodies by weight. To make a human requires a spectacular array of compounds made up of around 60 different elements. Deficiencies of any of these elements causes health problems and disease but a lack of oxygen will kill you in minutes.

Oxygen has two forms. The most common form is a pair of oxygen atoms O2. This colourless, tasteless gas makes up 20% of the air we breathe. O2 is unusual by any standards. The six electrons in the outer shell of each of the two atoms combine is such a way to result in one lonely electron on each atom (known as a free radical). Electrons hate being on their own and will go out of their way to find a partner to the extent that they will kidnap electrons from other pairs. Having two free radical electrons on one O2 molecule gives oxygen its manic qualities. O2 will react with almost anything it bumps into to kidnap an electron and this is blandly referred to as oxidation. In practice oxidation can mean oxygen combining with food we have eaten to give us energy, to clothes fading through oxidation of dyes, rust through oxidation of metals and explosions through (rapid) oxidation of fuels.

Another curious feature of having two free radical electrons is that O2 is paramagnetic meaning that when in a magnetic field O2 also becomes a magnet. Liquid O2 (formed at -183 degrees Celsius) will form a liquid bridge between the two poles of a horse-shoe magnet. Before rushing out to try this yourself please note the beautiful pale blue liquid O2 is a more concentrated form of the gas. Something that burns in air becomes explosive when soaked in liquid O2. The memory of a liquid O2 soaked hob-nob biscuit burning and spinning like a Catherine-wheel will live with me for a long time.

It is only through photosynthesis that such a reactive element can be so abundant in our atmosphere. Without plants, bacteria and algae producing oxygen for us to breath all the oxygen in the atmosphere would have reacted with elements in the earth long ago and life on this planet would have taken a very different evolutionary path.

Another form of oxygen is ozone or O3. Formed by high energy UV light hitting the upper reaches of our atmosphere. Ozone is an even more reactive form of oxygen and makes O2 look calm and well adjusted by comparison. In the upper atmosphere ozone protects us from cancer causing UV light by absorbing most of the radiation before it reaches us on the ground. At ground level ozone becomes more troublesome. It is formed by UV light reaching ground level on sunny days and as a bi-product in car exhausts. Ozone has a distinct chlorine bleach smell and its highly reactive nature means it damages our lungs when breathed in. O3 has been linked to asthma attacks and other severe respiratory problems and is considered a pollutant at ground level.

Tune in next week for frightening fluorine.

@RotwangsRobot

Images by @SciCommStudios

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Nitrogen

Nitrogen as an element is stubborn and uncommunicative. It’s rudeness stems from the triple bond between the identical twin atoms. The bond is so strong it can’t be broken easily which excludes reactions with all other elements. For all intents and purposes nitrogen behaves like a noble gas. It makes up around 78% of the Earth’s atmosphere and every breath we take and our lungs don’t even notice. A room filled with nitrogen and no oxygen can kill anyone who enters it in a few breaths with no apparent distress to the victim because our body, unable to react with nitrogen, can’t detect that anything is wrong.

The official discovery of nitrogen is credited to Daniel Rutherford (apparently no relation of Ernest Rutherford of atomic structure fame) in 1772. Discovery is perhaps a bit strong to describe what Rutherford achieved. Rutherford found that there was a portion of air that did not allow a flame to burn and killed any mice placed in a jar containing this strange new gas (most of this portion of air was later proved to be nitrogen). Many other eminent scientists were carrying out similar experiments at the time but no one could figure out what was going on. Theories such as ‘de-phlogisticated air’ and ‘mephitic air’ or azote (meaning ‘lifeless’) were bandied about but a name ‘nitrogen’ was finally given to this gas in 1794 by Jean-Antoine Chaptal after nitre as nitric acid could be shown to contain the mysterious gas.

An unreactive nature and relative abundance means nitrogen is often used to protect substances from reactive oxygen. The gas inside crisp packets is nitrogen to stop the crisps going soft and soggy and petrol is stored under a blanket of nitrogen to stop unwanted reactions with oxygen. When cooled down to -196 degree Celsius nitrogen becomes a liquid similar in appearance to water. Using liquid nitrogen to freeze food preserves it better than putting it in a standard freezer. The extreme cold freezes the water molecules in food quickly and goes some way to prevent the ice expanding and breaking apart the cell structures within the food which would normally turn it mushy when warmed up again. The nitrogen won’t react with the food to spoil it and simply evaporates leaving no residue when warmed up.

The character of nitrogen changes completely when combined with other elements to form compounds but to achieve this is no mean feet. To split up nitrogen twins there are two approaches. Plants use method one; quiet, calm negotiation through nitrogen fixing enzymes. These enzymes are actually found in a nitrogen fixing bacteria that lives in a symbiotic relationship in the root nodules of certain plants. Their subtle persuasion gently prizes apart the three strong bonds between the two nitrogen atoms.

Method two is rather more dramatic and pretty much comes down to brute force. By piling in a huge amount of energy the bonds can be ripped apart and forced in to forming new bonds with other elements. Nature does this through lightning. Thousands of volts of power ripping through the air pull apart the nitrogen twins and the free nitrogen atoms join up with oxygen and hydrogen to form nitrates and ammonia that gets washed down in the rain.

Original Harber Reactor at BASF

Humans like a challenge and faced with an abundant but unreactive element tried their damnedest to get the twins to play with the other kids. The problem was solved by Fritz Haber in typical human style – punish, beat and torment nitrogen until it has no other choice (similar sentiments are often expressed by students learning the Haber Process for chemistry exams). Nitrogen and hydrogen molecules are ‘kettled’ in to a tiny space (high pressure) and bated (heated) into a seething mass of anger. The molecules are pinned to an iron catalyst (adsorption) where the bonds between the atoms start to break and reform. Some nitrogen atoms will react with the hydrogen atoms and, one hydrogen atom at a time, nitrogen becomes ammonia (NH3). Despite all of this only around 15% of the nitrogen can be persuaded to react. Any unreacted nitrogen simply gets cycled round again and again until it relents.

The Haber Process is now used to produce 500 million tonnes of ammonia and ammonium nitrate worldwide every year and is almost identical to the 1909 process developed by Haber himself. This has allowed the manufacture of fertilizers on such a scale and has lead to the huge global population growth of the 20th Century as we are now able to feed far more people than ever before. Haber’s great innovation created headlines like ‘Bread from air’. All of this should be fairly familiar to GCSE students. What isn’t discussed as much is the use of ammonia in the production of explosives but I’ll talk about that more in another post on Fritz Haber.

Next week we get radical, it’s oxygen!

@RotwangsRobot

Image from Dr Ian Hamerton via @SciCommStudios

Carbon

Carbon is the child prodigy of the periodic family. Imagine Leonardo da Vinci, Marie Curie, Thomas Edison and Stephen Fry all rolled in to one person and you are starting to get a glimpse of the greatness. Approximately one third of the discipline of Chemistry is devoted to the compounds of carbon – ‘Organic Chemistry’ is loved and loathed by chemists and volume after volume can be found on the subject in any even vaguely scientifically inclined university library. To give a comprehensive overview of this extraordinary element is work for generations of  scientists and writers far better than me. Instead I am going to try and pick on some of the features that make carbon so interesting.

As an element carbon can be dull coal or glittering diamonds (there are stories of girls of the Moulin Rouge throwing diamonds in to the fire to watch them burn). Carbon can also take more exotic forms as in Bucky balls (nano-scale footballs of carbon), graphite (in your pencil lead) or graphene (a single sheet of graphite).

Carbon has been known about since prehistoric times but the most recent form, or allotrope, was discovered in 1985. Considering all these different forms are made of only one element the range of their properties is staggering. Crystal clear diamonds are the hardest known naturally occurring material, its name is Greek for unalterable or unbreakable, and pure diamonds are excellent insulators. Opaque graphite is soft and greasy and conducts electricity (if you have a potato clock at home you can swap one of the metal connectors for a sharpened pencil and it will work just as well. If you have a diamond ring you can try the same trick but the potato clock won’t work. People may also look at you strangely as you twist your jewellery in to a raw potato).

The compounds of carbon are even more numerous and diverse. From sugars to proteins to DNA there are more compounds of carbon than you can poke a stick at – even the stick will have a huge number of different carbon compounds within it. All of this comes from the fact that carbon has four electrons in its outer shell (in between the complete and perfect shells of helium and neon) and all capable of forming a pair with an electron from another atom. You can stick four different atoms to each carbon and then you can form long chains, circles, cages, sheets etc. etc.. The mind boggles at the versatility.

Perhaps the most curious result of this friendly and all inclusive attitude to bonding with other atoms is the ability of carbon to form ‘handed’ or chiral molecules. If you take a good look at your hands (perhaps in the privacy of your own home to avoid awkward moments at work or on the tube). You will notice that they are mirror images of each other and no amount of twisting and turning can make a left hand look like a right hand. The four major components of your hands (fingers, thumb, palm and back) all point in different directions and are like the four different atoms, or groups of atoms, bonded to a chiral carbon atom. So what I hear you bellow.

Chiral carbon would be an interesting aside in the chemistry of this element if it wasn’t for the fact that every living thing on this planet has a preference for one hand. The everyday examples of this are the 90% of humans who are predominantly right-handed. 90% of sea shells twist in a right-handed (dextral) orientation. Left-handed coiling shells (sinistral – the origin of the word sinister) are highly collectable. On the supra-molecular level 100% of all living organisms have one hand of DNA. Many molecules in your body are handed and rarely occur naturally with both ‘hands’ present.

With so many of the molecules in your body being ‘one-handed’ this can have implications when introducing new handed molecules in your food or as therapeutic drugs. To illustrate the problem find someone you know reasonably well and shake hands with them. Ignoring the social awkwardness of the situation as long as you shake right to right or left to left the hands should fit together comfortably. Shaking a left hand with a right hand is not so easy and the hands won’t fit together so well. The same can be true on the molecular level causing significant problems.

A classic example of a simple chiral compound we eat in food is carvone. The right handed molecule smells like caraway but the left smells of spearmint. Another deceptively simple chiral molecule is thalidomide – a drug given to hundreds of pregnant women in the late 1950s to treat morning sickness with tragic consequences. One hand of thalidomide is indeed effective against against morning sickness but the other hand causes severe birth defects. Both forms are chemically identical and no-one at the time considered they would have any significantly different biological function – hindsight is a wonderful thing. Unfortunately you cannot give just one form of thalidomide to a patient as it will convert to both forms inside the body. All chiral drugs are now rigorously tested in both forms before being released on to the market.

There is still hope for thalidomide though this will be of little comfort to those living with the consequences of its previous use in the 1950s. It has proved an effective treatment for leprosy and, with careful warnings for any women taking the drug not to start a family whilst receiving treatment, thalidomide can still do some good.

Next week is nitrogen – bland and innocuous or creepy identical twin?

@RotwangsRobot

Images by @SciCommStudios

The Atom

The structure of atoms and the arrangement of the periodic table are intimately linked. Trying to blog the characteristics of the elements without an explanation of how all atoms are structured is becoming impossible so… Think of this as a blue print of the atom – but drawn with a crayon, gripped chimp-like in my left hand.

The Duplo kit for building atoms would contain only three types of building blocks.

Protons

The number of proton defines the identity of the atom (which element in the periodic table).

Each proton has a charge of +1 and an atomic mass of 1. Protons are found in the centre of an atom in the nucleus and absolutely hate being held so close to each other. Imagine having several magnets and trying to push all the north poles together in a very very small space – this is how reluctant protons are to be near each other only more so. Neutrons are included in the nucleus to mediate the situation. The more protons you have the more neutrons are needed to stop the protons splitting off from the main group (radioactive decay).

Neutrons

The UN peacekeepers of the subatomic world.

Each neutron has a mass almost the same as the proton. As their name suggests neutrons are completely neutral so the number included in the nucleus of the atom will have no influence on the identity of the atom and little impact on its personality. This is how hydrogen can have none, one or two neutrons in its nucleus and still be hydrogen and behave almost exactly the same even if it has put on a bit of weight.

Electrons

Give atoms their personality.

Electrons are light and fast moving but trapped on a fixed path orbiting around the nucleus (think hamster in a wheel). Electrons have a charge of -1 so the number of electrons equals the number of protons to give an atom with no overall charge. If the atom (beryllium) has four protons (+4) it will have four electrons (-4) in what is technically called the zero oxidation state – Be(0).

More than one hamster on a wheel is ridiculous so things need to be organised. Electrons are arranged into shells and subshells in a 2, 2 + 6, 2 + 6, 2 + 10 + 6, 2 + 10 + 6,…. pattern. If you read the periodic table from left to right as you would words in a book, starting from hydrogen you will see that the number of elements in each block matches the pattern of electrons in shells. This is not a coincidence.

For example, …

Hydrogen – 1 electron – 2 wheels, 1 hamster

Helium – 2 electrons – 2 wheels, 2 hamsters running in opposite directions. Symmetrical and even – this is a complete shell.

Lithium – 3 electrons – 2 wheels, 2 hamsters running in opposite directions; 2 bigger wheels, 1 hamster. A wheel without a hamster is a sad sight so lithium will readily give away its outermost hamster (electron) to obtain a complete shell of hamsters and wheels.

Beryllium – 4 electrons – 2 wheels, 2 hamsters running in opposite directions; 2 bigger wheels, 2 hamsters running in opposite directions.

And so on and so on…… This arrangement of wheels and hamsters is called the ‘Pauli Exclusion Principle’ – use it in conversation, impress your friends.

All atoms are aiming for an ideal number of electrons 2, 10, 18, 36, 54 etc. as this number gives full outer shells like the enviable Noble gases. To achieve this atoms towards the left side of the periodic table will give electrons away to reach one of the magic numbers (for example, sodium with 11 electrons will give away one to reach the happy number 10). Elements to the right of the periodic table will take electrons (fluorine will steal one electron to make up a total of 10) and elements in the middle will share with other atoms to give the outward appearance of completeness.

The by-product of all this electron swapping and sharing is chemical bonds and molecules or compounds and an entire scientific discipline.

@RotwangsRobot

Images by @SciCommStudios

Boron

Boron is like the shy kid who is quietly good at most subjects in school.  Unlike most of the other elements Boron is not born in stars but was first created in the Big Bang and continues to be made by cosmic rays  in deep space or the upper reaches of Earth’s atmosphere. Despite its relatively low abundance and low profile boron has found its way in to many aspects of our everyday life and for many of us we don’t even notice.

Boron’s quiet brilliance and versatility all stems from its being three electrons away form the ‘ideal’ helium structure. Giving away three electrons is a big ask, especially when that only leaves you with two, so boron likes to share. Boron will share each of its three outer electrons in exchange for a share of an electron from three other atoms (totalling six). Admittedly some elements are very selfish and tend to the hog the electrons offered by boron but others are more generous. Boron will even shuffle everything round to accommodate two electrons from one donor atom to make up a full, happy, complete shell or octet. See supplementary post on atomic structure for a better explanation (due later this week).

Boron’s uses include: Pyrex (or borosilicate) cookware in your kitchen as it is more resistant to thermal shock than conventional glass; neodymium magnets (and you thought they just contained neodymium); insecticides (in the form of boric acid); bullet proof vests (in the form of boron carbide) and to keep swimming pools clean (again in the form of boric acid).

There is a good chance that boron is also sitting in your washing powder, in the form of sodium perborate, ready to do its bit oxidising, and thereby bleaching, stains on your washing. You may also have seen boxes of borax in pharmacies allegedly for use in laundry but I suspect most of these are now sold to teachers and parents wanting to do ‘goo‘ demonstrations with their kids.

Boron also forms compounds with hydrogen called Boranes which, similarly to their carbon equivalents, burn to release a huge amount of energy. The story I was told as an undergraduate went something like this. During the height of the cold war an American spy managed to sneak in to a rocket testing facility in Russia. Whilst there he observed a test launch and to his surprise saw green flames billowing out of the rocket’s thrusters. He quickly sent a message back to America describing his observations and American scientists deduced that the Russians were experimenting with borane fuels. These highly reactive compounds were known to be very effective rocket fuels but were difficult to handle and toxic. The Americans had carried out relatively little research up to then, and loathed to be left behind by the Russians, they began pouring money into researching borane technology.

It later emerged that the spy was colour blind and that the flames he had observed were orange all along. The use of boranes as fuel for rockets and aircraft, like the Lockheed SR-71 ‘Blackbird’, seems to have ended. However, boron still occasionally makes a star turn in pyrotechnics such as flares and fireworks – just look for the characteristic green flames.

Brace yourself for greatness. Next week its carbon.

@RotwangsRobot

Images by @SciCommStudios

Beryllium

Beryllium’s glamorous lifestyle hides a dark character. Though sweet on the outside it is very nasty underneath.

On Earth, and in the rest of the universe, beryllium (Be) is rare. With four electrons beryllium is only two electrons away from a happy stable arrangement like helium. It is fairly easy for beryllium to lose these two electrons to form Be2+ and form bonds with other atoms to make compounds. This means all the beryllium found naturally on earth is tied up in compounds with other elements. The most common place to find beryllium, for those rich enough, is in emeralds. It is also found in a range of other gemstones with the names varying with the colour. The colours have nothing to do with beryllium but come from trace impurities such as chromium or manganese in the crystals.

The element beryllium is a metal with some unusual properties. Beryllium is light, strong and has a high melting point which makes it an ideal choice for the space industry. Rocket nozzles made with beryllium alloys don’t deform under the high temperature conditions they experience.

A more unusual use of the metal is as windows for X-ray detectors and as the beam pipe for the Large Hadron Collider. The LHC has a huge doughnut shaped pipe through which scientists accelerate protons towards each other (I like to think of the protons as two piñatas smashed together to find out what’s inside). Because beryllium metal is strong and inflexible high vacuums can be created inside the pipe, the particle debris from the proton collisions are very small, as is the nucleus of beryllium, meaning the particles travel through the beryllium pipe to the detectors relatively undisturbed.

Space vehicles, big budget physics and jewellery – so far so glitzy. What about the dark side?

Beryllium and its compounds are toxic. Be2+ is very similar in size and character to magnesium, in the form of Mg2+, which carries out a huge number of vital functions in the human body. Be2+ will be absorbed by the body mistaking it for Mg2+ but it won’t work as well leading to a breakdown in vital processes at a cellular level. Beryllium’s rarity means we will not be exposed to dangerous levels in our everyday life but metal workers in the space industry were once at greater risk of exposure – beryllium is particularly dangerous when its dust is inhaled. Huge improvements in working practices in the space industry have now reduced the risks to a minimum.

The cruel twist to poisoning cases is that many compounds of beryllium taste like sugar. When the element was first discovered it was suggested its name should be glucinum or glucinium after the Greek word for sweet.

There are no recorded cases of deliberate beryllium poisoning but this isn’t surprising. Although the sweet taste would mean beryllium would be easy to disguise in food it would be a poor choice for wannabe poisoners. Beryllium’s rarity is an insurance against murder but its high melting point means it is also very difficult to work with. The first ever ingot of beryllium was cast in 1898, 70 years after the initial discovery of the element.

Next week, its not boring, its boron.

@RotwangsRobot

Images by @SciCommStudios

Lithium

Lithium (Li) is a soft metal, has low density and is highly reactive with water. It has two party tricks. One, when lithium compounds are burnt they burn with a bright red flame – never go to a fireworks display with a chemist, they will suck all the fun out of the experience by telling you which elements have been used to make the different colours. The other trick you may have seen in your chemistry lessons at school. Small lumps of lithium metal would have been cut with a knife from a larger stick and then dropped into a dish of water. The lithium fizzes and skims its way across the surface of the water like a demented water boatman.

To me lithium is like a naïve kid, eager to please and in awe of helium (the cool and aloof distant cousin). Lithium tries to mimic helium by giving away one of its three electrons to any other atom that will take it. As is often the case with two people wearing identical clothes, one will look effortlessly sophisticated, while the other will look faintly ridiculous. Lithium looks ridiculous. Just because lithium is wearing the same number of electrons as helium does not mean they look the same.

Giving away and sharing electrons are how atoms make friends. Losing an electron leaves the atom with a positive charge, in this case Li+, which is attracted to any atom or molecule with a negative charge. Giving away an electron also makes Li+ very small and it is often dwarfed by the atom that has taken its electron making a very uneven pairing. Li+ still sticks loyally to its domineering partner. This generosity means you will never dig up a lump of lithium the way you could a nugget of gold. If most of the lithium on the planet is in the form Li+ we should talk about some of the things Li+ can do.

Lithium’s willingness (or desperate need for appreciation) to give away its electron means it is a great candidate for use in batteries. Electrical energy is simply something that has a charge which is moving. This can be the electron from lithium moving towards another element that will accept it. This is how disposable or coin batteries work. In the rechargeable batteries we have in laptops and mobile phones it is the Li+ that shuttles between the positive and negative ends of the battery (depending on whether it is being charged or being used).

The most unexpected use of lithium is in the treatment of mental illness. Lithium has been found to be most effective in the treatment of Bipolar disorder. Li+ is the active ingredient in the drug lithium carbonate but no one knows exactly how it works. The important bit is that it works and lithium carbonate is the standard by which all new drugs for treating Bipolar disorder are judged. The pharmaceutical use of lithium is all the more surprising because it has no known biological role in the human body. Studies with rats seem to show a need for a very small amount of lithium in their diet (equivalent to about 1mg per day for humans) but the reasons for this are unclear.

Next week’s blog post is to die for! Its Beryllium.

@RotwangsRobot

Images by @SciCommStudios