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I'm a Chemistry student learning about periodic trends. I know that in (many organisms') cellular respiration, oxygen serves as the final electron acceptor due to its high electronegativity.

However, applying the periodic trends, fluorine is more electronegative than oxygen, and the noble gas neon even more so than fluorine. Why aren't either of these the final electron acceptor? I know that in some organisms, the final electron acceptor is sulfur. But I've never heard of it being fluorine or neon. Why?

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One of the main reasons that modern(!) biology uses oxygen as an electron acceptor is availability.

Around 2.45 billion years ago, oxygen (O$_2$) started being built up in the atmosphere (which actually killed off a lot of the lifeforms/bacteria at that point). Since then, oxygen consuming lifeforms were able to establish themselves. Before that, most organisms probably used mainly (elemental) hydrogen as electron acceptors.

Apart from not really being available in the atmosphere, there are other reasons why fluorine or neon don't make for good biological electron acceptors:

  • While elemental fluorine (F$_2$) is indeed extremely electronegative, this makes it so reactive that it:
    a) could not be controlled by biology [the reactivity of oxygen is why it killed so many bacteria in the first place] and
    b) just does not occur (or at least remain in) in the elemental state in nature (there is no measurable F$_2$ in our atmosphere).
  • Neon (and other noble gases) are in theory also quite electronegative, actually so much so, that they never* occur without their electrons and therefore don't react at all.

*It's somehow possible to form noble-gas compounds, but it requires very specific chemical reaction conditions, that mostly occur under controlled man-made conditions (and are not good for biological life forms).

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    $\begingroup$ I suspect another reason is simple availability. Oxygen is the most abundant element in the Earth's crust, fluorine is relatively rare (> 0.1%), and tightly bound in compounds. $\endgroup$
    – jamesqf
    Nov 13, 2018 at 18:19
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    $\begingroup$ There are instances of fluorine gas found in nature (within certain minerals) but they are pretty rare. YouTube and press releases 1, 2 $\endgroup$
    – uhoh
    Nov 14, 2018 at 5:21
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    $\begingroup$ Note that oxygen was available to organisms well before the GOE, merely in bound form. $\endgroup$
    – DevSolar
    Nov 14, 2018 at 12:45
  • $\begingroup$ Yeah, try breathing F2, it won't be fun. $\endgroup$
    – tox123
    Nov 14, 2018 at 14:50
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Availability and applicability.

Availability.

In the beginning, there was CO2. It was abundant in the atmosphere, and later, the oceans.

Fluorine and neon weren't, and so respiration evolved around what was (and is) available.

Ref.: Paeloclimatology / History of the Atmosphere.

Applicability.

The other point about oxygen is that it works rather beautifully both ways. Chloroplasts can easily split up CO2 and H2O into glucose and O2 with a bit of sunlight. Hemoglobin can combine both O2 and CO2 with just a little difference in partial pressure. Mitochondria can run through the citric acid cycle without getting destroyed in the process.

Once fluorine has taken hold of another atom and formed a molecule, it will be pretty hard for an organism to make it let go again, and if it does the fluorine will want to react with something, anything really, whether that's good for the organism or not.

On the other end, neon doesn't want to react with anything.

So while chemically there's a point to be made for the more energetic oxidizer, evolution / an organism is not "interested" in the energy content alone. The substance must be available, and the process must be somewhat sustainable. Oxygen ticked those boxes, fluorine and neon didn't.

Even rocket scientists, who are really looking for the most energetic compounds they can get their hands on, dropped the idea of fluorine as a propellant because it's not safe to handle in uncombined form. There's a lesson in there.

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    $\begingroup$ I think the rocket scientist example is flawed, because these rocket scientists happen to belong to a biological system that has evolved using oxygen. Reasoning after the fact of evolution under oxygen availability is not telling that evolution under predominant fluorine availablity couldn't have lead to (other, functioning) biological systems. To point out another example: H₂O is really a very aggressive and corrosive solvent. But we are perfectly adapted to deal with it and use it, and thus it is fine for us, whereas, say, H₂S is not. However, already if you'd ask some sulfur-oxidating... $\endgroup$
    – cbeleites unhappy with SX
    Nov 15, 2018 at 18:26
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    $\begingroup$ ... bacteria, their "point of view" will differ considerably. $\endgroup$
    – cbeleites unhappy with SX
    Nov 15, 2018 at 18:32
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    $\begingroup$ @DevSolar: of course. As modern chemist I'd start by guessing cell walls of teflon to contain HF solution. I.e., while of course I cannot say how nor whether things would have evolved, I'd expect a fluorine-based biology to be all in all more "harsh" (in a similar sense as that our oxygen-based biology uses more harsh chemistry than the sulfur based (nowadays) niche biological systems), but then the whole organisms would probably be more "fluorinated" and thus able to cope with fluorine/HF. (Also, on the one hand the difference in electronegativity between oxygen and fluoride is less than that $\endgroup$
    – cbeleites unhappy with SX
    Nov 15, 2018 at 18:50
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    $\begingroup$ between sulfur and oxygen, but at the other hand, there's the step from divalent to monovalent which would be a major difference). Also, the aggressivity may be offset to a certain extent because we may be looking at systems that work in much colder temperatures: 20 °C is the boiling point for HF, melting point is below -80 °C. Stepping down a few 10s of °C may be slowing down reactions to a suitable pace. Who knows? Summary: HF/F₂ based biology would surely look quite diffrent from "our" biology. But that doesn't mean it cannot work. $\endgroup$
    – cbeleites unhappy with SX
    Nov 15, 2018 at 18:56
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    $\begingroup$ @DevSolar: no, sorry: I like your answer - no need to edit. The point of my comment is just that the alien rocket scientist (or combustion engine engineer) from the HF-planet may think fluorine a totally normal oxidizing agent... (and may have trouble if that bit of H₂O they have gets into the HF in their system...) $\endgroup$
    – cbeleites unhappy with SX
    Nov 15, 2018 at 19:28
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The atomic radius of fluorine is just slightly larger than that of carbon. When a fluorine atom bonds to a carbon atom that is part of a carbon backbone, the fluorine atom covers up not only the C-F bond but also the adjoining C-C bonds. This makes it impossible for biological enzymes to access these bonds to break them, and is why fluorinated compounds are biologically inert.

This is the reason why we fluoridate water and toothpaste; bacteria have no enzymes that can break down enamel that is formed with fluorine! It is also why teflon (repeating units of -CF$_2$-) is not biodegraded yet saturated fatty acids (repeating units of -CH$_2$-) are easily biodegraded.

All elements that are used biologically have ecological cycles where they are reused for other purposes. Because fluorinated compounds can't be broken down, such an ecological cycle would rapidily come to a halt. Therefore, fluorine has an evolutionary disadvantage over other elements.

I agree with the other answers that neon can't be an electron acceptor because it won't form into compounds. I disagree with their "oxygen first" argument; evolution doesn't care which mechanisms evolve first. If a fluorine metabolic pathway had been more effective than oxygen's, its pathway would eventually surpass the earlier-evolved pathway. Furthermore, there are plenty of trace minerals (e.g. selenium) that are used by life.

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    $\begingroup$ Evolution does somewhat care about which mechanism evolves first: it tends to seek a local optimum, not a global optimum. If the benefits of an oxygen pathway and a fluorine pathway are similar, and both are a major advantage over whatever came before them, evolution is likely to get "stuck" on whichever one evolves first. $\endgroup$
    – Mark
    Nov 14, 2018 at 0:22
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    $\begingroup$ @Mark True, but then you get something like the evolution of photosynthesis, and everything gets thrown out of whack planet-wide. It's not inconceivable that the same thing could happen with something like fluorine, if it were available. The availability argument is much stronger - regardless of utility, life can't use it if there's no source for it. The proportions of elements in life are pretty close to the proportions of biologically available elements (e.g. including the "no enzymes" argument) in Earth's soils and oceans. $\endgroup$
    – Luaan
    Nov 14, 2018 at 14:53
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Neon just does not work as an electron acceptor. It is that inert that there are currently no known Neon compounds at all.

Fluorine would work in principle, but it is rare compared to oxygen and its strong reactivity makes it a very dangerous substance in elementary form. So it seems very natural that life chooses Oxygen and not Fluorine.

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    $\begingroup$ Of course, oxygen is also a horribly dangerous substance - it's just that evolution created life that's able to cope with it. Even then, it's a balancing act and oxygen (and oxygen compounds) are responsible for quite a few cell deaths and cancerous growths :P The Great Oxygenation Event killed of almost all life on Earth's surface/oceans. But granted, coping with fluorine would be even worse, and perhaps impossible (under standard pressure and temperature). $\endgroup$
    – Luaan
    Nov 14, 2018 at 14:48
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The reason is, free Fluorine does not exist in nature and Neon is a noble gas. I would make the assumption, that oxygen is the only free and abundant electron acceptor in our biosphere.

1) Fluorine reacts with every element with only a few exceptions (some noble gases) and will thus be bound instantly even if it is constantly produced somewhere.

2) Because of its electronegativity the energy to free Fluorine from complexes is very high, so efficiency of photosyntheses will be shitty.

3) Under the assumption there would be an atmosphere of fluorine gas, carbon based life could not exist, because fluorine reacts with carbon already below room temperature.

The comment below stating that fluorine is rare is plain wrong. It is not as common as oxygen, but doesn't need to be. E.g. carbon is also rare in comparison to oxygen. The main problem is lack of accessibility due to stability and high energy necessary to free it, connected with the fact that it would destroy every protein. A suitable electron acceptor must be metastable and be able to co-exist with carbon based life.

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    $\begingroup$ Free oxygen also didn't exist in nature when life first formed. It needed to be liberated through photosynthesis. The more important thing is that fluorine is very scarce even in compounds, compared to something like oxygen. While its abundance would be enough if it had a micro-nutrient role, it certainly isn't enough for something like being the final electron acceptor. And then there's the other tens of reasons why fluorine wouldn't work, like the fact that it (and its compounds) don't dissolve in water... $\endgroup$
    – Luaan
    Nov 14, 2018 at 15:00
  • $\begingroup$ Whatever, free fluorine never existed and therefore it never was an option. It will also never be an option, because even if it would be produced by plants, it would react instantanously with something else. This means it will be never a free electron acceptor. Nowhere in the universe. $\endgroup$
    – user40249
    Nov 14, 2018 at 15:41
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    $\begingroup$ This source request is silly. $\endgroup$
    – user40249
    Nov 16, 2018 at 12:59

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