exchemist

This has prompted me to revise the bonding scheme for transition metals with carbon monoxide: https://en.wikipedia.org/wiki/Metal_carbonyl This involves a dative σ-bond from the lone pair on C to the metal and a π back bond from occupied d orbitals on the metal to low-lying π* antibonding orbitals on CO. So donation of an electron pair in both directions, preserving neutrality overall. The effect of the involvement of the antibonding orbital is to weaken the C≡O bond (nominally triple in the free CO molecule) and strengthen the M-C bond. This I think gives a clue as to how such metal atoms can weaken the N≡N triple bond (preparatory to adding H atoms), N≡N being isoelectronic with C≡O. It starts to become clearer........ N.B. The need for an electron pair in a metal d-orbital to make the back-bond requires the metal to be in a low oxidation state.

I haven't seen any mention of Ni in the paper or the Wiki article on nitrogenases that I quickly read to try to understand more about them. But it is interesting I think to reflect on how many of these heavy metals play such critical roles in life. We often think in terms of H, C, N, O, S, and P, plus a handful of s-block cations, but actually a huge array of heavy elements gets pressed into service as well. Their multiple oxidation states and d orbitals turn out to be pretty important.

Yes I think there is a reference in the paper on the other thread about the means organisms use to keep oxygen away from the active centre. I can imagine that a metal site that can bind N2 might also bind O2 - even might prefer to do so - which would stop it working. (Reminiscent of how carbon monoxide blocks haemoglobin, though perhaps not an exact parallel.) In chemical terms it's really fascinating, since the N-N triple bond is so notoriously hard to break.

OK, I've now started a thread on the evolution of nitrogenase, in the Evolution section of Biology. I knew nothing about this at all until a few days ago. 😀

Following on from @Moontanman's thread on a new nitrogen-fixing organelle, I started wondering how biological nitrogen fixation first arose at the dawn of life. I found the linked paper, which I thought very interesting on the subject: https://www.sciencedirect.com/science/article/pii/S0966842X23000914 The writers focus on the metal atoms (or metal/sulphide complexes) which are at the heart of nitrogenases, which can bind nitrogen, lower the strength of the triple bond and progressively add H+ and electrons to form eventually 2 molecules of ammonia. There are 3 variants of nitrogenase, one using just Fe, one using Fe and Mo (molybdenum) and one using Fe and V (vanadium). I was surprised to see these 2 transition metals have such a biologically important role, but there you go. It seems there is evidence the first nitrogenase appeared in the Archaean, before the Great Oxygenation Event (i.e. global-scale photosynthesis), which I suppose is not a surprise, seeing as a lot of life would be needed to geo-engineer the planet, and that would require a lot of fixed nitrogen. They suggest that, before the GOE, there would have been a lot of Fe²⁺ in the oceans, whereas under oxidising conditions this would go to Fe³⁺, the salts of which tend to precipitate from aqueous solution, so would be less bio-available. So a system incorporating Fe is not hard to explain. Curiously, though, phylogenetic analysis suggests that the version incorporating Mo as well as Fe was the first to appear, even though the concentration of Mo in the early ocean was apparently very low. That version has better kinetics, which may have favoured it, but it still leaves open the issue of where the Mo came from. They speculate that there may have been higher local concentrations in the zones where the first nitrogenase arose, perhaps in hydrothermal vents. But this is very much open-ended and needs further research. By the way I found the chemistry of these nitrogenases really interesting. There seems to be some very unusual chemistry, involving bridged hydrides to supply the extra electrons needed for the reduction. But that's another subject. It seems the evidence is that nitrogenases are an "evolutionary singularity", meaning this little family of 3 closely related variants, using the 3 metal combinations mentioned, seems to have evolved once only in the whole history of life on Earth. But absolutely vital to the whole enterprise of course.

OK, but telephone numbers like this don't tell us a great deal until put into context. What concentration of NOx is this thought to have generated? Especially in the marine environment where life is thought to have started.

Hardly enough for much, I'd have thought. But maybe just enough to get some biochemistry started. I suspect N availability would have been one of the key constraints at the beginning. But I may have found a good paper on this. Let me read it and start a new thread if it's what I'm after.

Ah that's interesting. I didn't realise thermal conductivity of gases was proportional to specific heat capacity. So it is something to do with 3/2R rather than 5/2R, after all.

Actually this prompted me to wonder about where the "fixed", i.e. not molecular N2, nitrogen came from at the origin of life. It's impossible to construct terrestrial biochemistry without a source of this, whether from nitrites, nitrates or ammonia or something like that. Could be worth starting a thread on it.........I'll do some digging.

Agreed. I was referring to electrolysis processes involving CO2 such as those in the Wiki article, not to direct splitting into C and O.

OK I just about follow this, but the overall stoichiometry and thermodynamics won't be affected by the mechanism, even if various separate processes and intermediates are involved. If the starting material is carbohydrate and the waste products are hydrogen and CO2, there has to be a notional reaction scheme that accounts stoichiometrically for the relation between reactants and eventual products. That's the bit I want to understand.

Ah yes, higher mass would reduce diffusion rate. Re sound, I suppose an interface with a denser medium would create some partial reflection. But that’s just a guess.

I’ve just had some new windows fitted which have argon between the two layers of glass. I can’t find a good explanation for this on line. I would expect the heat capacity to be lower than for air, as argon is monatomic, but this does not seem likely to be relevant. Would argon conduct heat less well and if so, why? Some “explanations” say the higher density of argon is an advantage but I can’t immediately see why. I can see that an inert gas would not react over time with components of the frame and seals, but this does not seem to be the chief reason for its use. Lower heat and sound conduction seem to be the reasons given, but why would this be? Does anyone know?

As I understand it, waste. The overall process has to release energy to make ATP from ADP, as it is ATP that is the principal energy molecule driving biochemical processes. I believe I read once that the gas in farts contains a lot of hydrogen, presumably from anaerobic metabolism by gut microbes. A schoolmate once collected some over water in the bath and claimed he set light to it. Whether it gave the characteristic “squeaky pop” of hydrogen was not clear however.

OK, so what is the overall reaction then? My primitive understanding of convention respiration is it essentially reverses photosynthesis, i.e. CO2 + H2O <-> (CH2O)n + O2, in which (CH2O)n is a generic carbohydrate. This process seems to evolve both H2 and CO2. I suppose one could have (CH2O) + H2O -> 2H2 + CO2. Is that what happens? I wonder what ΔG is for a process like that. Suppose the entropy term at least will be favourable, since 3 small gas molecules are produced.

There is normally a reaction involving a metal catalyst that can adsorb the molecule and make it easier to split into ions, which is what you would need for electrolysis.

Expect you can buy neodymium alloy magnets on the internet these days. Make sure you don't trap your fingers. They can be a safety hazard.

How do you print a permanent magnet?

While there are electrolytic reduction processes for CO2: https://en.wikipedia.org/wiki/Electrochemical_reduction_of_carbon_dioxide. none of them seem to yield oxygen.

Yes I suppose that must be it. I was thinking of anaerobic bacteria that use alternative chemistry as fuel, like sulphate reducing or iron reducing bacteria.

From what I have just quickly read, these seem to have independently evolved, from mitochondria, several times in different species. So an example of convergent evolution, enabling their possessors to adapt to anoxic environments. What remains unclear to me is what the energy source is for their respiration. The flow charts I have seen seem to show pyruvate as the input, presumably from glycolysis. So that suggests glycolysis as usual, followed by some alternative to the Krebs cycle that does not require oxygen. Maybe someone can explain how this works. They don’t seem to be sulphate-reducing or anything like that.

OK. I suppose if there were a full stop after “human”, and if “believes” were rewritten as “beliefs”, it could be rendered partly intelligible, though the bit about faith and believes [sic] still doesn't seem to make a lot of sense in the context of the rest. Can you paraphrase it for my benefit, or get AI to do so?

Extremely interesting, thanks for posting this. It seems this may shed some light on very early evolutionary processes by which other organelles may have arisen, by being first endosymbionts and then getting integrated into the cell. I know next to nothing about this but I presume a key feature of the change would be the progressive migration of at least parts of the genetic coding needed for replication, from the endosymbiont to the nucleus of the host cell. I think I have read this is thought to have happened with mitochondria, which still retain some of their own DNA, separate from the cell nucleus. I see this work says that the template for some of the proteins the former endosymbiont needs is now in the cell nucleus, but a label is attached to them which gets them picked up by the "nitroplast". Perhaps investigation of this will help us understand how eukaryotes acquired other organelles in the long distant past.

Yes I think you have got it. I admit I don’t know how this is presented to students in the US today. My experience with Imperial units dates from schooldays in the UK in the early 1970s, when we transitioned from Imperial to metric. I remember how awful it was, compared to the simplicity of metric, and specifically, the version of metric that later came to be known as Systeme International (SI) units.

You are muddling metric and old-fashioned Imperial units. g in old units is 32ft/sec squared. g is 9.8 m/sec squared in modern SI units. If you multiply lb by g in old units you get the force in something called poundals, defined as the force needed to give a 1lb mass an acceleration of 1ft/sec squared. So there are 32 poundals in 1 lb-force. A pressure given in units of lb/sq in is implicitly in units of lb-force, not lb mass. lb-force is a force unit already, so no need to multiply by g. It’s a nightmare. If you really want to do your head in, read this: https://en.wikipedia.org/wiki/Poundal