I found a number of interesting papers during June, and I am reasonably pleased that there were no significant contradictions to my ebook Planetary Formation and Biogenesis.  There were three major thrusts. The first one involved fluid flow on Mars, which my work requires, although of course its existence is generally accepted. Observations from the Curiosity rover at Gale crater showed isolated outcrops of cemented pebbles and sand. The rounded pebbles in the conglomerate indicates substantial fluvial abrasion, which led the authors (Williams et al. Science 340: 1068 – 1072) to conclude that sediment was mobilized in water that probably exceeded the threshold conditions (depth, 0.03 – 0.9 meter, velocity 0.2 – 0.75 m/s) required to transport the pebbles. They conclude that sustained liquid water must have flowed across the landscape. Unfortunately, no evidence was available as to why it flowed, or what the fluid was. (It would be water, but such water could either be heated, or it could contain something to depress its melting point.) 
 
Another major issue is, when did rocky planets get their volatiles? Volatiles that are accreted from the stellar accretion disk are almost certainly essentially lot to space due to the high energy emissions of the young star, which persist for about  0.5 Gy. My mechanism of rocky planet formation requires many of the volatiles to accompany feldsic crust formation, and I required that to happen following about 4 Gy BP, in part to ensure that the chemicals required for life were available continuously from about 4 Gy BP for another 1.5 Gy. Pujol et al. (Nature 498: 87-89) measured argon ratios from gas occluded in rock, and concluded that less than 10% of feldsic crust evolved between 170 My and 3.8 Gy BP, 80+10% of the crust formed between 3.8 Gy and 2.5 Gy BP, and < 30% crust was generated from 2.5 Gy BP to today. These results effectively confirm that my requirements were met. Interestingly, Debaille et al (Earth Planet Sci. Lett. 373: 83-92) proposed that early-formed mantle heterogeneities persisted at least 1.8 Gy after Earth's formation. The best explanation is that there was a stagnant lid regime as the crust built up. The major change in geodynamics noted at ~3 Gy BP then reflects the transition to plate tectonics.
 
In my ebook, I argued that there should be significant reduced species emitted geochemically early in a rocky planet's history, and I argued that the components in the Saturnian system would convert methanol and ammonia to methane and nitrogen. I also argued that the planetary systems formed relatively quickly, as opposed to the current theories that require at least 15 My to get a giant. I was pleased to note that Malamud and Prialnik (Icarus 225: 763-774) calculated how serpentinization would produce nitrogen and methane in Enceladus, and argued that for their calculations to be correct, because initiation requires heat from short-lived radioisotopes, the Saturnian moons had to be formed between 2.65 and 4.8 My after CAI formation. Just what I needed! Etiope et al. (Icarus 224: 276-285) showed that methane may be formed at relatively low temperatures by the Sabatier reaction catalysed by chromite minerals. More good reduced materials.
 
Finally, Pringle et al. (Earth Planet Sci. Lett. 373: 75-82) showed from consideration of silicon isotopes in meteorites from 4-Vesta that Vesta differentiated under more reducing conditions than previously considered. Again, just what I wanted.
 

My previous post outlined the issue of the quadruple bond in C₂, and an interesting issue is, how do you visualize it? I think this is important because it permits the qualitative reasoning that may be more immediately useful to chemists, but there is something else. Sometimes, by looking at a problem in a different way, you get a different perspective. Thus through using the valence bond/hybridization perspective Shaik et al. (Nature Chem DOI:10.1038/NCHEM.1263) consider the bonds in C₂ as follows: a σ bond employing sp orbitals, accompanied by two π bonds arising from the pairing of two p electrons from each carbon atom, plus the additional electron in each carbon atom occurs in outward pointing hybrids, (i.e. with axes along the axis of the acetylenic cylinder). It would usually be considered that the directionality would prevent bond formation. Computations, however, show this is not the case.
 
In accord with the theme of this blog, is there an alternative way of looking at this? For me, yes, and it reminds me of my first theoretical paper! (Confession: not the best presented paper ever.) The problem then was that substituents adjacent to a cyclopropane ring experienced chemical effects different from those attached to an unstrained ring. These were being explained by partial charge delocalization from the cyclopropane ring, but my point was that the effects of strain were not properly considered. The changes in chemical effects were certainly explained in terms of an electric field at the substituent adjacent to a strained system that differed from that of a standard alkyl system, but the question was, was that due to charge delocalization, or to the strain energy? From Maxwell's electromagnetic theory, the work done moving electric charge behaves as if it is stored in an electric field derived from the accompanying polarization field. Charge was moved, but was the movement satisfactorily explained by constraining the movement to within the strained system?
 
To assess the strain energy, after a little mathematics and an assumption I subsequently did not find convincing, I came up with the strain energy being proportional to [sinθ/2]/√r, θ/2 being the angle that that bond deformed (θ the change of bond angle.) and r the new covalent radius. I was quite excited when I found out this was quite accurate; I was less so when I realized my "derivation" was simply too questionable. Accordingly, I simply placed it into the paper as an empirical proposition. However, if you take the bond energy scheme recently (then!) determined thermochemically by Cox, very good results were obtained for ethylene and acetylene. (That does not imply these systems did not delocalize electrons, but it did imply they did not if there was no adjacent unsaturation.)
 
Thus in this picture, acetylene was described as three bent sp³ bonds. As an aside, I could have made a prediction of the strain in [1,1,1] propellane, and I would have been the first to comment on it. Why didn't I? Partly because I never thought about it, but mainly because this part of the paper was an aside, to get the strain energy I needed. The objective was to calculate fields on adjacent substituents, and leaving aside the methylene carbons, there are no substituents adjacent to the junctions of a propellane, so that molecule was outside the scope of the paper.
 
Returning to C₂, the axial wave, containing the single electron is also inherently sp³ in this picture. Why that is relevant is that the sp³ wave has a primary wave with which everyone is familiar, but also a small lobe that is on the opposite side of the carbon atom. We get the fourth bond if these two small lobes constructively interfere. That argument says that a fourth bond is conceivable; what it does not show is whether the fourth bond has any net energy, and that requires calculation. It also requires a better definition of that small lobe. (Note that this picture is merely a different way of viewing the molecule. The concept of hybridization is simply one of combining component waves. When combining different waves of different energies, there are various ways that it can be done, provided the energies are properly accounted for.)
 
Does the different description offer anything? I think yes. In 2009 Wu et al. (Angew. Chem. Int. Ed. 48: 1407 –1410) describe the bond in [1,1,1] propellane as an inverted bond, i.e. they seem to consider the orbitals to have inverted and become directed inwards instead of outwards, however in my picture, it is a "normal" bond, derived from bicyclobutane, with all bonds more strained. However, it does explain why the "internal" bond in the propellane is relatively strong, and that in C₂ so weak. Of course, computations show this too, and in some ways more convincingly, nevertheless the qualitative view might at least show some experiments that might be worth doing. For example, if such an "sp³ orbital" were to invert, there would be a significant change in electric moment of the molecule, which, again from Maxwell's theory, would be promoted by the absorption of a photon. Thus suitable molecules should have a significant change in their UV spectra. Besides C₂, which in this picture should have relatively long-wavelength transitions, we might even consider something like 1,4-diazabicyclo[2.2.2]octane, even though it has two lone pairs with nowhere obvious to go. Tertiary amines usually have a weak UV absorption at about 215 nm, but for 1,4-diazabicyclo[2.2.2]octane I would expect the UV spectrum to show a significant spectral shift due to a new interaction between the nitrogen atoms. Would anyone care to run me a spectrum? I am curious now to see if this reasoning is correct.
 
Of course, the more thoughtful out there might argue that while the small lobe of an sp³ orbital might interfere, there is a reason they may not be capable of inverting in standard quantum mechanics. Can you see it?

In some of my previous posts, I have bemoaned the absence of public discussions between chemists on matters of theoretical importance to chemistry, and so, when one actually appears, I must first congratulate the participants and the journal. This specific issue relates to two recent discussions (Angew. Chem. Int. Ed. 52: 5922-5925; 5926-5928) relating to whether there is a quadruple bond in C₂. Whether the molecule is important is a matter of opinion, but the point that I have tried to make previously in these posts is simply publishing papers is not sufficient to lead to greater understanding. What I believe is needed is subsequent analysis, so that we better know what we know as opposed to what we think. It therefore follows that to be useful, the discussion should be in a form comprehensible to the educated chemist who is not directly involved in the field, and it is with in mind that I wish to consider, were the criticisms worth making, and were they answered satisfactorily in that the general chemist would learn anything? There are obviously other issues, but I shall leave them for further posts.
 
The first article was a criticism by Frenking and Hermann of a previous publication in which the existence of the quadruple bond was proposed. Their main points were:
(a)  The force constant of C₂ < force constant acetylene. The stretching frequency of C₂ was 1855 cm^-1 while that of acetylene is 1974 cm^-1. Their argument was that these data are evidence that the bond in C₂ is weaker than that of acetylene.
(b)  The claim for C₂ to have a stronger bond lies in measurement of the dissociation energies of acetylene. Thus when the first hydrogen is removed, the energy required is 133.5 kCal/mol, and the second 116.7 kCal/mol, a difference of 16.8 kCal/mol. This 16.8 kCal/mol is supposedly the additional energy arising from the formation of the quadruple bond, however the criticism is that the framework is not constant, in that in the second dissociation, the carbon-carbon bond length increases by 0.035 A. They argue there is no reason to assume that a smaller C – H bond dissociation energy arises through strengthening of the C – C bond; there may be other reasons.
(c)  The remaining arguments were largely dependent on computational procedures and they may or may not be correct. The outside observer merely has to either accept or not the points. However, there was one point made that irritated me. The criticism was that the original paper adopted incorrect reference states. In general physics, the end conclusion eliminates the frame of reference, and hence the results are independent of it. The reference points eliminated from the calculation are chosen for ease of calculation, and should not affect the conclusion.
(d)  In the footnotes, they write "A bonding model is not right or wrong, but it is more or less useful." Their argument is the quadruple bond model is not useful because it does not agree with the properties of the molecule. Whether or not this criticism is correct or not, it is important because it focuses attention on the critical issues that lead to further understanding.
 
The response by Danovich, Shaik, Rzepa and Hoffmann is of interest. They argue first that the rule that stronger bonds have stronger force constants may not be universal. Given that there is no firm relationship (at least that I know of) relating bond strength and stretching force constant, that may be true, but equally it may not. As an outside observer, I think the F&H point has validity, although it is not conclusive. They also argue that computations show that the energy change in the C – C distance changing from 1.21 to 1.24 A is negligible. If so, the point (b) fails. However, we must ask, were the computations 100% guaranteed true? I am not convinced. On the other hand, the lowering of the energy is unambiguous and uncontested, so any argument thereafter really must be based on what this means. The responders argue that this means additional bonding, and to defeat that argument, there has to be some alternative for this energy lowering.
 
Does it matter? I think conceptually, yes, because it makes us think more about what is a bond. (More on this in subsequent posts.) Consider the energy argument above, and transfer that to dinitrogen. The triple bond of N₂ is no simple extrapolation from single and double bonded nitrogen species. One likely reason is, like the acetylide anion, the triple bond configuration stabilizes the lone pair, and extrapolating Coulson's "bent bond" model, the orbitals in the triple bond are bent away from the lone pair, thus exposing the lone pair electrons to greater positive field.
 
The skeptical chemist should now ask, what is the exact electron configuration in C₂? Are all electrons paired? Unfortunately, this was not specifically stated in the article, however by observation the species is actually a singlet. To be a singlet as opposed to being a triplet diradical, within standard MO theory, the two electrons must be in a common wave function. If they are, it is either bonding or antibonding, and since there is a net energy lowering, it must be bonding. So, within MO theory, the fourth bond exists because there is an energy lowering of 16 kCal/mol. Suppose we wish to go outside MO theory. If so, and have the two electrons in separable wave functions, then to get a singlet there has to be a phase relationship between the two waves, and an interaction that leads to the energy lowering, and if so, the question then is, why is that not within the description of a bond? In fact Shaik et al. (Nature Chem DOI:10.1038/NCHEM.1263) show by VB treatment, that the reality is in line with that proposition. Thus I believe this omission of the singlet nature of the state was unfortunate, because it is the omitted observational evidence that settles the issue, at least for me.
 
Finally, a quote from Roald Hoffmann: Could it be that “this most rigorous theory,” the one that affords “deep insight,” in fact has failed (so far) to provide pragmatic chemists with a way of thinking about real chemistry—whether it is that of “synthetic” or of short-lived molecules—that is as useful as are Lewis structures, arrow-pushing, and molecular orbitals?
 
My guess is, so far, yes, but if we had more of these discussion-type articles more directed towards the general chemist, perhaps the answer would change.

A comment on a previous post suggested the process of science funding was faulty, so I thought I should comment on a situation that is occurring here (New Zealand). I have no idea how general this is, but I think it is serious, not because of what is happening, but rather what is not happening. If scientists wish to keep being funded from the public purse, I think they have to make certain the outward perception is one of dynamism and value and that the money is advancing something.
 
About a year ago, the Prime Minister announced that the government would put an additional sum (about 4% of science budget, plus or minus quite a bit because of certain vagueness in the announcement) for the express purpose of doing something new. He then asked the public to submit challenges for this money. So far, surprisingly good! For once, the public is involved! We can always quibble about the amount of money, but recall that right now we have something resembling an economic crisis throughout the world, particularly relating to government debts, so such quibbles border on the pathetic. We should be grateful for what comes!
 
The problem soon surfaced. A large number of challenges were submitted, and an expert committee was set up to sort through these. Eventually, ten were published as successful. My guess is that none of these were actually submitted by the public, because they all looked like they came from a committee. Like motherhood and apple pie, you could hardly dispute that they were important, but on the other hand, there was a total lack of originality, incisiveness, etc. What I suspect happened is that the best of what was received was put into a blender and mush emerged. While it may be quite reasonable to blend in everyone's ideas, on closer analysis, it ended up appearing to be “feel-good” money to be spread around existing science organizations to continue doing more or less what they were doing. This image was not helped when I heard on a radio program a representative say this work was important, and just because such programs already had funding, that was no reason not to spend more money on them.
 
That is all very well, but I think there were several negatives from this. The first is, a number of citizens spent quite a bit of their own time putting together challenges, and wading through the “bureaucratic-speak”, and I feel they deserve better than to be simply ignored later. If nothing else, a response thanking them for their efforts, and explaining why what was accepted was felt to be more important than what they submitted. Most people would accept the concept that if someone put in something that was reasonably more important, it should win. The second main one is that it looks as if the original purpose has been subverted for the benefit of institutions. The third one is that the winners are so vague they cannot be measured, therefore there is no way that the government can later say the exercise was a success. These are very important reasons. Scientists have to accept that it is important to carry the public with them, and when the government gives money, it is important to give the government something to promote now and boast about later. As yet, no money has been allocated. What I think should happen is when it is allocated, it is done so with public fanfare, to give the impression that something good could arise from this. What should not happen is that the allocation gets buried in a pile of bureaucratic files. I do not know how general this problem is, but I do not see a lot of platform-building for science going on anywhere.

For May, once again there were few significant papers (at least that I found) that impinge on theories of planetary formation, and I shall restrict myself to the two closest. A commonly measured variable is isotope enhancements, and Halliday (Nature 497: 43-44) showed that lunar basalts have slightly higher levels of heavy iron than Earth, which is itself significantly enhanced in heavier isotopes compared with Mars or Vesta, however there is no enhancement for heavier isotopes in lithium. What does that mean? Interpreting such results is a common problem, because what we are trying to do is to get whatever we can from the very limited samples available to us. The temptation then is to look at the current model and fit the data to it, and if it makes sense within that model, than that is how the data are interpreted. We tend to assume that isotope enhancements only arise through vaporization/condensation, but there are alternative ways of enhancing heavier isotopes, such as the chemical isotope effects. In short, such enhancements may reflect greater processing of a sample.
 
Another interesting paper came from Hamano, Abe and Genda (Nature 497: 607 – 610). They classified rocky planets according to their distance from the star. A type 1 planet forms beyond a critical distance and solidifies within several million years and if the planet acquired water during formation, it retains it. A type 2 planet lies within the critical distance, and can maintain a magma ocean for up to 100 My because the steam atmosphere (assuming it acquired water) blankets the planet, and incoming radiation from the star exceeds the radiative ability of the atmosphere to emit sufficient heat to cool the surface (~ 300 W m^-2). Hydrodynamic escape dessicates type 2 planets. Venus is on the border of the critical distance, but is classified as Type 2 because of its properties. The argument depends on there having been a magma ocean in the first place, and it only applies to water emitted at the very beginning. On Earth, volcanism has been emitting volatiles continuously, and while most are secondary now, some remain primary. The point is, most volatiles have yet to be degassed at 100 My. On Mars, it appears to have taken up to 500 My before the bulk of the water was degassed, by which time their mechanism is irrelevant. Of course, what they tried to do was work out why Venus is like it is. My argument is that there are alternative interpretations to the data, and in the case of Venus, it never had much water on the surface.
 
Meanwhile, for those interested in some of the issues relating to planetary formation and the origin of life, there is currently a forum operating on the web. Go to https://astrobiologyfuture.org/forum . Amongst other things, people are more prepared to ac=knowledge what we do not know, and more prepared to be speculative, than in scientific papers.