an autodidact meets a dilettante…

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exploring oxygen

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I’d much prefer choccy cigars


I’ve been reading David Beerling’s fascinating but demanding book The Emerald Planet, essentially a history of plants, and their contribution to our current life-sustaining atmosphere, and it has inspired me to get a handle on atmospheric oxygen in general and the properties of this rather important diatomic molecule. Demanding because, as always, basic science doesn’t come naturally to me so I have to explain it to myself in great detail to really pin it down, and then I forget. For example, I don’t have any understanding of oxidation right now, though I’ve read about it, and probably written about it, and more or less understood it, many times. Things fall apart, and then we fall apart…

Okay, let me pull myself together. Oxygen is a highly reactive gas, combining with other elements readily in a number of ways. A bushfire is an example of oxidation, in which free oxygen is ‘consumed’ rapidly, reacting with carbon in the dry wood to produce carbon dioxide, among other gases. This is also called combustion. Rust is a slower form of oxidation, in which iron reacts with oxygen to form iron oxide. So I think that’s basically what oxidation is, the trapping of ‘free’ oxygen into other gases or compounds, think carbon monoxide, sulphur dioxide, hydrogen peroxide, etc etc. Not to mention its reaction with hydrogen to form water, that stuff that makes up more than half our bodily mass. 

Well, I’m wrong. Oxidation doesn’t have to involve oxygen at all. Which I think is criminally confusing. Yes, fire and rust are examples of oxidation reactions, but so is a reaction between hydrogen and fluorine gas to produce hydrofluoric acid (it’s actually a redox reaction – hydrogen is being oxidised and fluorine is being reduced). According to this presumably reliable definition, ‘oxidation is the loss of electrons during a reaction by a molecule, atom or ion’. Reduction is the opposite. The reason it’s called oxidation is historical – oxygen, the gas that Priestley and Lavoisier famously argued over, was the first gas known to engage in this sort of  behaviour. Basically, oxygen oxidises other elements, getting them to hand over their electrons – it’s an electron thief. 

Oxygen has six valence electrons, so needs another two to feel ‘complete’. It’s diatomic in nature, existing around us as O2. I’m not sure how that works – if each individual atom wants two electrons, to make eight electrons in its outer shell for stability, why would it join with another oxygen to complete this outer shell, and then some? That makes for another four electrons. Are they now valence electrons? Apparently not, in this stable diatomic form. Here’s an expert’s attempt to explain this, from Quora

For oxygen to have a full outer shell it must have 8 electrons in it. But it only has 6 electrons in its valence shell. Each oxygen atom is actively seeking to get more electrons to complete its valence shell. If no other atoms except oxygen atoms are available, each oxygen atom will try to wrestle extra valence electrons from another oxygen atom. So if one oxygen atom merges with another, they “share” electrons, giving both a full outer shell and ultimately being virtually unreactive.

For a while this didn’t make sense to me, mathematically. Atomic oxygen has eight electrons around one nucleus. Six in the outer, ‘valence’ shell. Molecular oxygen has 16 electrons around two nuclei. What’s the configuration to make it stable? Presumably both nuclei still have 2 electrons configured in their first shells, that makes 12 electrons to make for a stable configuration, which doesn’t seem to work out. Did it have something to do with ‘sharing’? Are the shells configured now around both nuclei instead of separately around each nucleus? What was I missing here? Another expert on the same website writes this:

[The two oxygen atoms combine to] create dioxygen, a molecule (O2) in which both oxygen atoms have 8 valence electrons, so they are happy (the molecule is stable).

But what about the extra electrons? It seems I’d have to give up on understanding and take the experts’ word, and I hate that. However, the Khan academy has come to the rescue. In video 14 of his chemistry series, Khan explains that the two atoms share two pairs of electrons, so yes, sharing was the key.  So each atom can ‘kind of pretend’, in Khan’s words, that they have eight valence electrons. And this is a covalent bond, unlike an ionic bond which combines metals with non-metals, such as sodium and chloride. 

Anyway, moving on. One of the most important features of oxygen, as mentioned, is its role in water – which is about 89% oxygen by weight. But how do these two elements – diatomic molecules as we find them in our environment – actually come together to form such a very different substance?

Well. According to this video, when H2 and O2, and presumably other molecules, are formed

electrons lose energy to form the new orbitals, the energy gets away as a photon, and then the new orbitals are stuck that way, they can’t undo themselves until the missing energy comes back.

This set me on my heels when I heard it, I’d never heard anything like it before, possibly because photon stuff tends to belong to physics rather than chemistry, though photosynthesis rather undoes that argument…

So, sticking with this video (from Brigham Young University Physics Department), to create water from H2 and O2 you need to give them back some of that lost energy, in the form of ‘activation energy’, e.g by ‘striking a match’. The video turns out to be kind of funny/scary, and it again involves photons. After the explosion, water vapour was found condensing on the inside of the glass through which hydrogen was pumped and ignited…

Certainly the demonstration was memorable (and there are a few of these explosive vids online), but I think I need more theory. Hopefully I’ll get back to it, but it seems to have much to do with the strong covalent bonds that form, for example, molecular hydrogen. It requires a lot of energy to break them. 

Once formed, water is very stable because the oxygen’s six valence electrons get two extras, one from each of the hydrogens, while the hydrogens get an extra electron each. The atoms are stuck together in a type of bonding called polar covalent. Oxygen is more electronegative than hydrogen, meaning it attracts electrons more strongly – the negative charge is polarised at the oxygen, giving that part of the molecule a partial negative charge, with a proportional positive charge at the hydrogens. I might explore the effects of this polarity in another post.

The percentage of oxygen in our atmosphere seems stable at 21% – that’s to say, it appears to be the same now as when I was born, but that’s not a lot of time, geologically. The issue of oxygen levels in our atmosphere over geological time is complex and contested, but the usual story is that something happened with the prokaryotic life forms that had evolved in the oceans billions of years ago, some kind of mutation which enabled a bacterial species to capture and harness solar energy. This green mutation, cyanobacteria, gave off gaseous oxygen as a waste product – a disaster for other life forms due to its highly reactive nature. The photosynthesising cyanobacteria, however, multiplied rapidly, oxygenising the ocean. Oxygen reacted with the ocean’s iron, creating layers of rust (iron oxide) on the ocean floor, later visible on land through tectonic forces over the eons. Gradually over time, other organisms evolved that were adapted to the new oxygen-rich atmosphere. It became an energy source, which in turn produced its own waste product, carbon dioxide. This created a near-perfect cycle, as cyanobacteria required CO2 as well as water and sunlight to produce oxygen (and sugar). Other photosynthesising water-based and land-based life forms, plants in particular, emerged. In fact, these life forms had harnessed cyanobacteria as chloroplasts, a process known as endosymbiosis. 

I’ll end this bitsy post with the apparent fact, according to this Inverse article, that our oxygen levels are actually falling, and have been for near a million years, and that’s leaving aside the far greater effects due to human activity (fossil fuel burning consumes oxygen and releases CO2). Of course oxygen is very vastly more abundant in the atmosphere than CO2, and the change is minuscule on the overall scale of things (unlike the change we’re making to CO2 levels). It will make much more of a difference in the oceans however, where the lack of dissolved oxygen is creating dead zones. The article explains:

 The primary contributor to these apocalyptic scenes is fertilizer runoff from agriculture, which causes algal blooms, providing a great feast for bacteria that consume oxygen. The abundance of these bacteria cause O2 levels to plummet, and if they go low enough, organisms that need it to survive swim away or die.

Just another of the threats to sea-life caused by humans. 

Written by stewart henderson

September 16, 2018 at 4:20 pm

Posted in environment, science

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On electrickery, part 1 – the discovery of electrons

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Canto: This could be the first of a thousand-odd parts, because speaking for myself it will take me several lifetimes to get my head around this stuff, which is as basic as can be. Matter and charge and why is it so and all that.

Jacinta: so let’s start at random and go in any direction we like.

Canto: Great plan. Do you know what a cathode ray is?

Jacinta: No. I’ve heard of cathodes and anodes, which are positive and negative terminals of batteries and such, but I can’t recall which is which.

Canto: Don’t panic, Positive is Anode, Negative ICathode. Though I’ve read somewhere that the reverse can sometimes be true. The essential thing is they’re polar opposites.

Jacinta: Good, so a cathode ray is some kind of negative ray? Of electrons?

Canto: A cathode ray is defined as a beam of electrons emitted from the cathode of a high-vacuum tube.

Jacinta: That’s a pretty shitty definition, why would a tube, vacuum or otherwise, have a cathode in it? And what kind of tube? Rubber, plastic, cardboard?

Canto: Well let’s not get too picky. I’m talking about a cathode ray tube. It’s a sealed tube, obviously, made of glass, and evacuated as far as possible. Sciencey types have been playing around with vacuums since the mid seventeenth century – basically since the vacuum pump was invented in 1654, and electrical experiments in the nineteenth century, with vacuum tubes fitted with cathodes and anodes, led to the discovery of the electron by J J Thomson in 1897.

Jacinta: So what do you mean by a beam of electrons and how is it emitted, and can you give more detail on the cathode, and is there an anode involved? Are there such things as anode rays?

Canto: I’ll get there. Early experiments found that electrostatic sparks travelled further through a near vacuum than through normal air, which raised the question of whether you could get a ‘charge’, or a current, to travel between two relatively distant points in an airless tube. That’s to say, between a cathode and an anode, or two electrodes of opposite polarity. The cathode is of a conducting material such as copper, and yes there’s an anode at the other end – I’m talking about the early forms, because in modern times it starts to get very complicated. Faraday in the 1830s noted a light arc could be created between the two electrodes, and later Heinrich Geissler, who invented a better vacuum, was able to get the whole tube to glow – an early form of ‘neon light’. They used an induction coil, an early form of transformer, to create high voltages. They’re still used in ignition systems today, as part of the infernal combustion engine

Jacinta: So do you want to explain what a transformer is in more detail? I’ve certainly heard of them. They ‘create high voltages’ you say. Qu’est-ce que ça veux dire?

Canto: Do you want me to explain an induction coil, a transformer, or both?

Jacinta: Well, since we’re talking about the 19th century, explain an induction coil.

Canto: Search for it on google images. It consists of a magnetic iron core, round which are wound two coils of insulated copper, a primary and secondary winding. The primary is of coarse wire, wound round a few times. The secondary is of much finer wire, wound many many more times. Now as I’ve said, it’s basically a transformer, and I don’t know what a transformer is, but I’m hoping to find out soon. Its purpose is to ‘produce high-voltage pulses from a low-voltage direct current (DC) supply’, according to Wikipedia.

Jacinta: All of this’ll come clear in the end, right?

Canto: I’m hoping so. When a current – presumably from that low-volage DC supply – is passed through the primary, a magnetic field is created.

Jacinta: Ahh, electromagnetism…

Canto: And since the secondary shares the core, the magnetic field is also shared. Here’s how Wikipedia describes it, and I think we’ll need to do further reading or video-watching to get it clear in our heads:

The primary behaves as an inductor, storing energy in the associated magnetic field. When the primary current is suddenly interrupted, the magnetic field rapidly collapses. This causes a high voltage pulse to be developed across the secondary terminals through electromagnetic induction. Because of the large number of turns in the secondary coil, the secondary voltage pulse is typically many thousands of volts. This voltage is often sufficient to cause an electric spark, to jump across an air gap (G) separating the secondary’s output terminals. For this reason, induction coils were called spark coils.

Jacinta: Okay, so much for an induction coil, to which we shall no doubt return, as well as to inductors and electromagnetic radiation. Let’s go back to the cathode ray tube and the discovery of the electron.

Canto: No, I need to continue this, as I’m hoping it’ll help us when we come to explaining transformers. Maybe. A key component of the induction coil was/is the interruptor. To have the coil functioning continuously, you have to repeatedly connect and disconnect the DC current. So a magnetically activated device called an interruptor or a break is mounted beside the iron core. It has an armature mechanism which is attracted by the increasing magnetic field created by the DC current. It moves towards the core, disconnecting the current, the magnetic field collapses, creating a spark, and the armature springs back to its original position. The current is reconnected and the process is repeated, cycling through many times per second.

A Crookes tube showing green fluorescence. The shadow of the metal cross on the glass showed that electrons travelled in straight lines

Jacinta: Right so now I’ll take us back to the cathode ray tube, starting with the Crookes tube, developed around 1870. When we’re talking about cathode rays, they’re just electron beams. But they certainly didn’t know that in the 1870s. The Crookes tube, simply a partially evacuated glass tube with cathode and anode at either end, was what Rontgen used to discover X-rays.

Canto: What are X-rays?

Jacinta: Electromagnetic radiation within a specific range of wavelengths. So the Crookes tube was an instrument for exploring the properties of these cathode rays. They applied a high DC voltage to the tube, via an induction coil, which ionised the small amount of air left in the tube – that’s to say it accelerated the motions of the small number of ions and free electrons, creating greater ionisation.

x-rays and the electromagnetic spectrum, taken from an article on the Chandra X-ray observatory

Canto: A rapid multiplication effect called a Townsend discharge.

Jacinta: An effect which can be analysed mathematically. The first ionisation event produces an ion pair, accelerating the positive ion towards the cathode and the freed electron toward the anode. Given a sufficiently strong electric field, the electron will have enough energy to free another electron in the next collision. The  two freed electrons will in turn free electrons, and so on, with the collisions and freed electrons growing exponentially, though the growth has a limit, called the Raether limit. But all of that was worked out much later. In the days of Crookes tubes, atoms were the smallest particles known, though they really only hypothesised, particularly through the work of the chemist John Dalton in the early nineteenth century. And of course they were thought to be indivisible, as the name implies.

Canto: We had no way of ‘seeing’ atoms in those days, and cathode rays themselves were invisible. What experimenters saw was a fluorescence, because many of the highly energised electrons, though aiming for the anode, would fly past, strike the back of the glass tube, where they excited orbital electrons to glow at higher energies. Experimenters were able to enhance this fluorescence through, for example, painting the inside walls of the tube with zinc sulphide.

Jacinta: So the point is, though electrical experiments had been carried out since the days of Benjamin Franklin in the mid-eighteenth century, and before, nobody knew how an electric current was transmitted. Without going into much detail, some thought they were carried by particles (like radiant atoms), others thought they were waves. J J Thomson, an outstanding theoretical and mathematical physicist, who had already done significant work on the particulate nature of matter, turned his attention to cathode rays and found that their velocity indicated a much lighter ‘element’ than the lightest element known, hydrogen. He also found that their velocity was uniform with respect to the current applied to them, regardless of the (atomic) nature of the gas being ionised. His experiments suggested that these ‘corpuscles’, as they were initially called, were 1000 times lighter than  hydrogen atoms. His work was clearly very important in the development of atomic theory – which in large measure he initiated – and he developed his own ‘plum pudding’ theory of atomic structure.

Canto: So that was all very interesting – next time we’ll have a look at electricity from another angle, shall we?


Written by stewart henderson

October 1, 2017 at 8:14 pm