Alternative interpretations

C2

Mon, 17 Jun 2013 03:45:01 +0100

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.

Posted by Ian Miller
Jun 17, 2013 3:45 am

Science funding

Sun, 09 Jun 2013 23:38:09 +0100

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.

Posted by Ian Miller
Jun 9, 2013 11:38 pm

Planetary formation update - May

Mon, 03 Jun 2013 03:19:16 +0100

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.

Posted by Ian Miller
Jun 3, 2013 3:19 am

Comprehensible quantum mechanics?

Sun, 26 May 2013 23:58:30 +0100

In the May edition of “Chemistry World” there was an item regarding “leaps of faith” in quantum mechanics, and this item quoted a paper published in Proc. Nat. Acad. Sci. showing how the Schrodinger equation can be arrived at from the classical Hamilton Jacobi equation. What puzzled me was, why was this published? After all, in the chapter “Classical Mechanics” in “Fundamental Formulas of Physics” (Dover, 1962), essentially the same thing was published, and no claim to originality was made. The book was a summary of well-known physics, so this was presumably well-established by then. So, why is quantum mechanics so weird? One possibility is that it is not at all weird, and requires no great leaps of faith at all. The only problem is that we do not understand it, which in turn might mean nothing more than there is more to sort out. One problem was that we were deeply committed to Newtonian mechanics, so anything non-Newtonian was, perforce, weird. Within its set of assumptions, Newtonian mechanics are, in my view, completely correct, but as I noted in my ebook, Elements of Theory 1, there are two statement implied by Newtonian mechanics that are not correct. The first is, force acts instantaneously at a distance. By far Einstein’s greatest contribution to science was to propose that that was wrong, and force is mediated at a velocity. Further, the statement that when you see something, you cannot say, “It is there,” but rather, “It was there when the photons set off.” The second erroneous assumption is inherent to Newton’s first law. Newton’s first law is often regarded as a bit redundant, because it is essentially the second law with a zero applied force. However, there is one further part to Newton’s first law, and that is that motion is continuous. In more detail, what the physicists call action is continuous. In my opinion, that is wrong, and it is where the problems in comprehension lie. Instead, I regard action as discrete, and specifically, in units of Planck’s quantum of action. That, as far as I can tell, is the only required difference between classical and quantum mechanics. The derivation of the Schrodinger equation immediately follows from the Hamilton-Jacobi equation if the quantum of action defines a period of the wave. The Uncertainty Principle and the Exclusion Principle also follow. I think another problem in understanding what is going on follows from an obsession with another part of Hamiltonian mechanics, namely the canonical equations. You will often see that these partial differential equations enable us to represent momentum, p, and positional coordinate, q, as equivalent, from which we can make phase space diagrams, etc. However, action is an integral of motion, and if the discreteness of action is the fundamental essence of quantum mechanics, then some care has to be taken with conclusions based on partial differentials. An example I gave in the ebook is this. ∫pdq has a simple meaning: a particle travelling along a coordinate with uniform momentum. Now, consider ∫qdp; a particle at constant position with a continual change of momentum? Strictly speaking, both integrals give you action, except one is ridiculous. As for the first, ∫pdq, consider that if you integrate over a period you should get a wavelength. If so, pλ = h, the quantum of action, and we have the de Broglie equation. Action can also be represented as ∫Edt, where E is the energy. If τ is the periodic time, then it follows again that Eτ = h, from which, bearing in mind frequency is 1/τ, then E = hν, as required. This does not require "leaps of faith", and is reasonably straightforward, but how many chemists get shown things like that in their courses on quantum mechanics? Oh no! What tends to happen is that massive equations get put up, or obscure formalism using the "Sledge Hammer" approach: "Trust me, I know what I am doing." Feynman said that nobody understands quantum mechanics. What I think he meant was that nobody as yet completely understands quantum mechanics, but I think you can get a lot closer to it if you take the trouble to get a few things in order. Ask what is really fundamental, and watch what follows.

Posted by Ian Miller
May 26, 2013 11:58 pm

Being discovered

Mon, 20 May 2013 04:25:51 +0100

Recently we have seen on the American Chemical Society website a sign “Publish Be Found or Perish”. This rings a bell with me because there is a similar discussion going on with book authors. Yes, you have to write something that is worth reading, either with books or with scientific papers, but the whole exercise is a waste of effort unless someone reads the work, and by definition, quality has nothing to do with the first reading because if you do not know what is in the paper or book, you do not now whether it has quality or not. So, how, as a scientist, do you get discovered? The short answer from me is, I do not know. With books, the best answer seems to be, “Get lucky!” The second best option is, “Be persistent!” This is, of course, what you have to do to maximize your chances of getting lucky. For any given time you do something, there is a certain chance that it will be noticed, so the more you do, the more chances. Publishing scientific papers in top journals probably helps. If you have a sequence of papers in one journal that is well-read in that topic, your name will eventually be recognized. Conference presentations probably help, because by circulating, people put a face to your name. Does anyone see a problem here? What you end up with is the people being found are the academics with lots of students working for them, and with good budgets for going to conferences. The problem is, those who are found that way are those who are known anyway. It becomes very difficult for the young scientist to be discovered, other than through being associated with someone famous. To be discovered by association means the discovered has almost certainly adopted the workings of his mentor, otherwise his name will not be on the papers. This reinforces the workings of “normal science” as defined by Kuhn, but the question then is, is that the way we want science to work? Do we want to have uniform acceptance of the current paradigm, or do we want to see whether we are missing something? The ones more likely to be original are the young scientists, because they have less invested in the current paradigm, but they are also the least likely to be found.

Posted by Ian Miller
May 20, 2013 4:25 am

Writing science to persuade

Mon, 13 May 2013 02:18:06 +0100

I recently became involved in a discussion on how to write a scientific paper, and the first thing I had to concede was that on the whole we do not do this well, and sometimes it is written almost as if the author said to him/herself, "Nobody will read it anyway." In many cases it may not matter. Many papers are written to archive an observation, or a procedure, such as how to synthesize something. These involve putting things down in the order that they were done, and making sure all terms are defined. The writing style probably does not matter much, because the only people who will read this are those who wish to either use the observation or to follow the synthesis. The first group will accept the statement and the second will have to work through it, no matter what. More difficult is when you have to interpret what you found. An obvious example is the structural determination. The problems include the fact that there will be several interpretations of any given observation. The usual approach is to eliminate them one by one, usually in a sequence of experiments, and if that is what you did, so must you report it. The major problems include a failure to eliminate all possible alternatives, in which case the report is unconvincing, or alternatively, the alternatives are eliminated, but the eliminations are scattered, and it is too difficult to keep them all in mind, in which case the argument runs the danger of being confusing. A common problem is the presentation of data that supports your hypothesis. It may, but equally it may support something else. Time for a confession! I once wrote a series of papers on the substitution patterns of red algal galactans. Prior to writing these, structural elucidation was very difficult. These initial procedures involved the molecules or substituted derivatives being broken down into fragments, following which a sequence of fragments were further fragmented, and from the resultant structures, the overall structure was inferred. Because there were so many different aspects that had to be kept in mind, in one paper I wrote with two others, in parts the sentences became so complicated that later even I had trouble working out what they meant. So I came up with an answer: represent everything mathematically. Rather than get to the structure linearly, I carried out a number of different operations on the parent molecule, and from nmr spectral data, each operation was consistent with a set of structures. The real structure was given when the intersection of all sets gave one element. I then wrote papers representing structural units as matrices and data as ordered sets. Mathematical manipulation was unambiguous. The problem was, the rather restricted audience was not very happy with discrete mathematics, and eventually an editor told me to stop doing that or else the papers would be rejected. As it happened, I did not care so I stopped publishing. I was self-employed, and this activity was to bring no income, so the decision to stop was not that difficult. The real shame was that the methodology was just becoming productive Nevertheless, this raises the problem, what concessions should be made to the reader? My view at the time was, the statement of what I believed the structure to be should be put down in the simplest form possible. However, while how I deduced them should be as clear as possible, I thought it is not unreasonable to expect some effort to be made by those who wished to question the structure. My view was that to put down mathematically the arguments leading to the structures was optimal because all logic steps are explicit and unambiguous. There is no question of acceptance; to disagree you must show some step does not follow. However, many scientists did not agree with such an approach, and prefer comfortable sentences, which will generally be read without questioning them. What do you think? Be unambiguous, but have few readers, or be comfortable but with questionable ability to convince?

Posted by Ian Miller
May 13, 2013 2:18 am

Planetary formation update - April

Mon, 06 May 2013 03:08:27 +0100

My ebook, "Planetary Formation and Biogenesis" was first published on Amazon 1 year ago, it argues that quite a lot of the standard theory needs rethinking, in particular that initial accretion is dependent on chemistry, not gravity, and while I have found a number of otherwise puzzling observations for the standard theory, as far as I can tell, nothing I have found contradicts my propositions. Readers may forgive me, but I find that rather satisfying. Part of the reason, of course, might be that the year has been relatively quiet regarding discoveries. That will change, because it is inevitable that sooner or later a large number of papers will come out regarding findings from Curiosity. That will be far more critical as far as my ideas go. A further possibility is that the theory is somewhat elastic, and hence difficult to falsify. That is true in some ways. There are a number of options for planets, but once one is chosen, there are very specific consequences. Unfortunately, some of those are as yet too difficult to test, which may also be why the theory has survived! The most interesting evidence came from the Kepler satellite. It discovered (Science 340: 262) that Kepler 62 has five planets that range from half to twice Earth's diameter. These are at 0.715, 0.427, 0.12, 0.929, 0.055 A.U., around a star of 0.69 times the sun's mass. It is estimated that the outer one is in the centre of the habitable zone, and the next inner one possibly. The problem then is, are these truly rocky planets or ice planets sent inwards according to one of the possible mechanisms proposed? If they are all rocky planets, and were spaced according to my "expectation prediction" (which requires the star to have accreted at a rate proportional to its stellar mass squared, which in turn is observed, but only loosely, so there should be a range from the expectation position) the typical planet equivalents should be Mars-type 0.58, Earth-type 0.328, Venus-type (if there is one, and this is somewhat flexible) 0.22, Mercury-type 0.12. (This also assumes the secondary accretion rate, critical for exactly how the rocky planet evolves, was similarly scaled to our star, and observational evidence shows a possible order of magnitude deviation each way.) If the outer one is the Earth-type, then the theory predicts that accretion was significantly faster, and any Venus-type should be at 0.47 A.U., and Mercury at 0.22 A.U. and there should be a Mars-type at about 1.14 A.U. Additional inner planets (Vulcans, which are predicted to be Mercury-like) would seem unlikely as the temperatures would grow too hot over a shorter radial difference. If the 0.427 A.U. planet is an Earth-type, then accretion was slower, and more material was available, in which case the Mars-type should be at about 0.68 A.U., the Venus-type at about 0.28 A.U., and the Mercury-type at 0.15 A.U. This agreement is not too bad, and the slower accretion rates could permit Vulcans. On the other hand, some of these bodies could be quite different, without violating the theory because if the accretion is slow, a variety of additional options might arise. Their densities should define their nature. Slower stellar accretion rates permit planetary bodies to grow bigger, at which point they interact chaotically. It is generally considered that one major body (Theia) collided with Earth and formed the Moon. However, it is possible that modest-sized bodies might have collided and retained much of their structure provided collisions were not too violent. There is evidence this occurred (Science 340: 22-24). The Earth's deep mantle behaves as if there are two major piles of different composition, one below Africa and one mainly below the South Pacific. Plumes rise from the edges of these and give rise to the volcanic islands. These piles are thousands of kilometers across, but their composition remains unknown. An important point is that these "piles" are denser than much of the remaining mantle. Within my proposition, this is suggestive that they accreted closer to the star than the bulk of the Earth, which increases the pyroxene content, they differentiated, then eventually collided with Earth. The increased density arises through shedding aluminosilicates during collisions, including shedding them to Earth's crust. Is that right? That is unknown, but it is an interesting thought, at least for me.

Posted by Ian Miller
May 6, 2013 3:08 am

"Scientists are snobs"?

Sun, 28 Apr 2013 23:34:45 +0100

In a previous post, I commented on an article in Nature by Robert Antonucci, in which he complained that only too many scientists do not spend enough time thinking, and are only too willing to accept what is in the literature, without checking. This was followed by another article by Keith Weaver, entitled "Scientists are snobs", who asserted that there was another problem: scientists are only too willing to believe that the best comes from the best institutions. This is also a serious issue, if true. Specifically, he complained that: (a) Scientists prefer to cite the big names, even when smaller names made the discovery, and the big names merely used it later. Yes, this may well be through sloth, and not doing a proper literature search, and in some ways it may seem not to matter. The problem is, it does when the original discoverer puts in a funding application. Too few citations, and the work is obviously not important – No funding! Mean while the scientists who did nothing to advance the technique gets all the citations, and the funding, and the conference invitations, and the "honours". The problem is thus made worse because of positive feedback. (b) An individual scientist gains more recognition if they work in a prestige institution. The implication is, the more prestigious the institution, the better the scientists. There is truth in that some scientists at more prestigious institutes are better, whatever that means, but if so, it is not because they are there, but rather the rich institutions pay more to the prestige scientists. (c) Even at conferences, scientists go to hear the “big names”, and ignore the lesser names. This is harder to comment on because I know that having been to many conferences, there are some names I want to hear, and many of the “unknowns” can produce really tedious presentations. Choosing sessions tends to be to maximize the chance of getting something from the conference. For me, the problem often ends up choosing between the big name, who as often as not will produce recycled stuff, or the little name, who may not have anything of substance. Conference abstracts sometimes help, but not always. What do you think about this? In my opinion, leaving aside the “sour grapes” aspect, Weaver raises an important point. The value of an article has nothing to do with the prestige of where it came from. To think otherwise leaves one open to the logic fallacy ad verecundiam. I wonder how many others fall into the trap Weaver notes? My guess is everyone is guilty to some degree of (c), but I do not regard that as a particularly bad sin. However, only citing big names is a sin. The lesser-known scientist needs citations and recognition far more than the big names. One might also notice that the greatest contributions to science have frequently come from almost anywhere. In 1905 the Swiss patent office was hardly the most prestigious source of advanced physics, but contributions from there changed physics forever. What is important is not where it came from, but what it says. Which gets back to where this post started: scientists should cover less ground and think more. Do you agree?

Posted by Ian Miller
Apr 28, 2013 11:34 pm

Do we learn from our mistakes?

Mon, 22 Apr 2013 04:49:59 +0100

Polywater might have been an obvious error for chemistry, but I still question, what did we learn from it? My guess is, not much. What we eventually realized is that while fused silica does not dissolve in water at any appreciable rate, it does if it is on the surface of a very small capillary. Why? Is it due to the curvature of the surface, or is a micro-column of water somehow more active? A general theory here could be of great help to medicine, or to much of research into nanotechnology, but such was the scorn thrown at polywater that a potential advance of great significance was dealt with like the baby discarded with the bath water. In previous posts I mentioned the problem of whether cyclopropane could delocalize is ring electrons into adjacent unsaturation. The textbooks say it can, and this is justified because MO theory says it can. Do you believe that? Are you still convinced when you are told that the computational programs that "settled" this issue were the same ones that asserted that polywater had very significant enhanced stability? The original MO treatment of cyclopropane was due to Walsh. His concept was that the methylene units were trigonal sp2 centres, with the third orbital of each carbon forming three-orbital overlap at the centre of the ring system. This left a p orbital on each methylene to overlap with the two p orbitals from the other methylene carbon atoms in partial side-on overlap. Since only two electrons were in the three-centre bond, there were four electrons for the three p-electron bonds, which led to two pairs for three bonds, one such bond being a "non-bond". These were obviously delocalized (assuming the model was correct in the first place) but the p orbitals were also properly aligned to overlap with adjacent p orbitals on unsaturated centres, so conjugation should follow. This was a perfectly good theory because it made predictions, however it is also imperative that such predictions were tested by observation. There is an obvious consequence to this theory. Perhaps the biggest reason cited for cyclopropane conjugation is that a cyclopropane ring adjacent to a carbenium ion centre has an additional stabilization of about 100 kJ/mol over other comparable carbenium ions. Of course electron delocalization might be the reason for this, but if it is, then the p electrons of the cyclopropane ring must become localized in the orbitals that can overlap with the carbenium centre, at least to some extent, therefore the “non-bond” must become localized, to the same extent, in the distal bond. With less electron density in the distal bond, it should lengthen. There have been alternative MO computations, which drastically shorten the distal bond, e.g. to 143.6 pm, but significantly lengthen the vicinal bonds e.g. to 159 pm (J. Am. Chem. Soc. 1982, 104, 2605-2612) although it is far from clear why this change of bond length happens. The predicted lengthening of the vicinal bonds presumably occurs because charge in them is delocalized towards the carbenium ion, but it is unclear to me why the "non-bond" shortens. As it happens, it is not important. A structural study has been carried out on such a carbenium ion, and the distal bond is so considerably shortened but the vicinal bonds are not so lengthened (J. Am. Chem.Soc. 1990, 112, 8912-8920). Accordingly, the computations are wrong. The polarization theory I mentioned in previous posts is in accord with this observation: the vicinal bonds remain unchanged because nothing much changes while the distal bond shortens because the positive field allows the electrons in the bond to align better with the internuclear axis. Now, the interesting point about this is that when the measurement was made, nobody questioned whether the Walsh MO theory might be wrong. Such is the power of established theory that even when observation brings in a result opposite to that predicted, and even when there is clear evidence (from polywater) that the computational methodology that led to this result is just plain wrong, we do not want to revisit it. Why is this? A general lack of interest in why things happen? Simple sloth? Who knows? More to the point, who cares?

Posted by Ian Miller
Apr 22, 2013 4:49 am

Polywater

Mon, 15 Apr 2013 00:59:21 +0100

I believe that just because everybody thinks standard theory is quite adequate, that is no excuse to reject a non-standard theory. On the other hand, many will argue that there is no need to fill the literature up with nonsense, so where do we draw the line? In my opinion, not in the right place, and part of the reason is that a certain rot in refereeing standards set in following the polywater debacle. Polywater was an embarrassment, and only too many referees did/do not want to be associated with a rerun. That, however, is no reason to adopt the "Dr NO" syndrome, namely that rejection guarantees the absence of a debacle. That policy would certainly have led to the rejection of Einstein's "Electrodynamics of bodies in motion". He was describing the dynamics of bodies without electric charge! And as for common sense, he was abandoning the principles of Galilean relativity and of Newton's laws of motion, both of which were "obviously correct". (Actually, he was abandoning the concept of instant action at a distance, which nobody really believed.) Anyway, back to polywater. This unfortunate saga began when Nikolai Fedyakin condensed water in or repeatedly forced water through quartz capillaries, following which Boris Deryagin improved production techniques (although he never produced more than very small amounts) and determined a freezing point of – 40 oC, a boiling point of ≈ 150 oC, and a density of 1.1-1.2. This was not water, but what else could it be? Everyone “knew” quartz was inert to water and there was no other explanation than the water had polymerized. Unfortunately, nobody thought to do an analysis for silicon. There followed the collection of considerable amounts of data, and in general these were correct (although the collection of an IR spectrum of sweat was probably not a highlight of science). Meanwhile a vast number of theoretical calculations emerged to “prove” the existence of polywater. So what went wrong? Apart from the absence of an analysis, not much initially. The referees had to accept that the experimental work was done satisfactorily. The computational work was simply a case of “jump on the bandwagon and verify what was known”. Unfortunately, those data were wrong. Nevertheless, the question might be asked, should the referees have permitted the computational papers? What the papers gave was the assertion that a certain program was applied, and this is what came out. In general, the assumptions were never clearly stated, nor were the consequences of the assumptions being wrong. The major problem with the computations was that, being based on molecular orbital theory, the proposed systems were assumed to be delocalized, and the calculations showed they were. As Aristotle remarked, concluding what you assumed is not exactly a triumph. The consequences of this unfortunate sequence of events were as follows: (a) Experimenter’s careers were wrecked. (b) Computationalist’s careers were unaffected. John Pople was relatively prominent in showing why there was considerable stability in water polymers, but that did not hinder his career (although his work on polywater did not feature strongly in his Nobel citation). (c) When exposed, work ceased. Nobody was ever interested in trying to work out why water in constrained space dissolved silica. (d) Little or no genuinely different theoretical work emerged in chemistry following polywater. (e) Most importantly, nobody ever stated what went wrong within the computations. In short, we learned nothing, or at least the general chemical community learned nothing. The question that must be asked regarding (d) is, was this because there is no further scope for theory in chemistry, and all that we can do now is deploy computational programs, have the referees killed any attempts, or have chemists simply lost interest? Your views?

Posted by Ian Miller
Apr 15, 2013 12:59 am