Is science sometimes in danger of getting tunnel vision? Recently published ebook author, Ian Miller, looks at other possible theories arising from data that we think we understand. Can looking problems in a different light give scientists a different perspective?

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I have seen some blogs from young chemists starting or being involved in their PhD who seem to think they have troubles so I thought that just in case they thought previous times were a golden age, why not disillusion them! This little tale also shows why I got addicted to alternative theories, and has two further messages for young chemists. (1) Give more thought to the importance of beginnings. It makes or wrecks (or lies somewhere in between) the rest of your life, so think! (2) Be careful what you wish for; sometimes you get it! Then it is too late to work out you might be better off without it.
I started my PhD at the end of 1963, but what preceded that is relevant because I started with baggage that most students do not have to carry. During the summer of 1962-3 (southern hemisphere!) I was given employment to assist a little research. The department had been involved with the Hammett equation, and had been looking at some benzylammonium dissociation constants. I had the job of purifying some and making some measurements, which I did, and which introduced me to physical organic chemistry and put my name on a paper for the first time. Then in my honours year, selenium poisoning due to the failure of fume cupboard ducting led to my missing lectures frequently. Then came disillusionment. A lecture on the quantum mechanics of the hydrogen molecule led to an equation across the blackboard, and the lecturer said that he would try to show how progress could be made in solving it. I stopped the lecture to point out the equation had an energy minimum when the internuclear distance approached zero, and where it was supposed to be infinite. (If you want to do theory, it helps if you can mentally determine critical aspects of a function.) The lecturer did not know what had gone wrong (and he was only lecturing QM because someone had to). I suddenly discovered that lecturers did not necessarily understand what they were teaching! And they were going to determine my honours level!
I wanted to understand, so later, once again sick, I thought, if wave particle duality occurs, as in diffraction, electrons do not have an option: they must follow what the wave requires of them. After all, no particle description gets diffraction. So, if the wave determines energy and momentum, why not consider the problem as a standing wave problem? (As an aside, can you think of a good reason why not? Bet you can't!) An important point about stationary waves is that they are single-valued, i.e., they do not self-interfere, which requires the geometry of the problem to fix the location of nodes and antinodes. (In a subsequent paper I submitted, I used an organ pipe as an example. The referee could not understand the relevance.) Now, for a given energy, to a first approximation in the Coulomb field of a hydrogen atom the momentum is independent of the mix of radial/angular momentum, so consider it angular, in which case wavelength is proportional to m(thetadot)r^2. Doubling the interactions (electron pairing) is equivalent to doubling mass, hence at constant frequency (frequency had to be conserved otherwise there would be self-interference and the wave would not be single-valued) the wavelength between the nuclei should be a/root2, where a is the Bohr radius. Then from the Einstein ratio, where energy = h x frequency, the energy of the component on the bond axis, in Cartesian coordinates had to be twice the energy of those components in the free atom, hence the bond energy of the hydrogen molecule was 1/3 the Rydberg energy. Try looking up the observed values – the agreement was extraordinarily encouraging, and I had this weird feeling that I had discovered something. Then, problems! The method did not work for any other bond, so it was wrong, right? Not so fast! For the alkali metals, the errors were a clear function of the quantum number n!
Now what? The next step was to go to the library. Unfortunately, with finals about five weeks away, most of the "good" books were gone. One that was there was by de Broglie, on his "double solution". The good news was that there was someone there who felt that there was a real wave there, which although not necessary for the above reasoning, seemed to be the only way there was a physical cause. The bad news was that it was clear that I needed to learn some more physics to make sense of quantum mechanics. One more thing was clear: I had to avoid quantum mechanics in my finals! So, when finals were over, and my total neglect of quantum mechanics had paid dividends, I had a decision: progress to PhD or go back and do physics. I decided to progress, and put my efforts to learn physics to one side. I could teach myself, so I thought. It turned out to be an interesting decision because I avoided bothering about the mathematical formalism of the state vector approach, which of course specifically forbids factorizing the wave function as I did above. My next problem was simple: choose a PhD project. More soon.
Posted by Ian Miller on Oct 12, 2012 10:54 PM BST
Since I found no papers that falsified the major premises, my alternative theory on planetary formation survived September! Of course the skeptic might say (a) I never found them, or (b) I ignored them. I cannot guarantee that (a) did not apply because I do not have access to every journal (nor the time to read them), but some, having read this month's Chemistry World, may accuse me of (b). This paper (Alexander et al. (2012) Science 337: 721) determined the isotope ratios of hydrogen and nitrogen in various bodies from the solar system with the goal of deciding from where Earth's water came. In particular, they determined that water from the outer solar system has a higher D/H ratio than Earth's water, and since hydrogen on Earth escapes to space, anything that creates hydrogen from water, such as UV photolysis, raises the D/H ratio. There is no known mechanism to lower it. Accordingly, they decided that their determinations falsify some modeling work, which has the volatiles arriving due to the influx of a massive amount of icy bodies during a period when Jupiter and Saturn migrated outwards (having previously migrated inwards!).  (For a planet to migrate outwards, conservation of angular momentum and energy require massive amounts of material from further out to be thrown inwards.)
So, where did Earth's volatiles come from? These authors determined the D/H ratio and the 15N/14N ratio in various types of asteroidal bodies, and found the ratios in CI chondrites closely matched the ratios of Earth's hydrogen and nitrogen. Therefore, on the basis that there were no further possible sources, they decided CI chondrites were the source of Earth's volatiles. If so, that falsified my theory. So, why did I ignore it? Basically because, in my ebook, I devoted a whole chapter with fifty-six references to this issue and most of the critical issues were ignored by this paper, which makes me a little grumpy about both the paper and the refereeing.
What can go wrong with this logic? First, simply matching two ratios runs into the possibility of the fallacy of false cause. The asteroidal bodies have a wide range of results, although the enrichment of one element tends to follow the other. Given a wide range, the value for Earth is likely to match one of them. However, if we compare total mass, the nitrogen/carbon ratios in such chondrites do not match the ratio on Earth by a factor of approximately four, which strongly suggests they are not the origin. Worse, the nitrogen/carbon ratio is almost four times higher on Venus, and two orders of magnitude lower on Mars, which requires each body to be struck almost solely by bodies of different origin and totally different composition. Then, to get the Earth's volatiles, Earth has to be struck by at least 10^23 kg of chondrite, and based on area the Moon would have been struck by about 7x10^21 kg of chondrite. There is no evidence to support this. Of course, CI chondrites are relatively rare in the asteroid belt, so we have to also ask, why did virtually all these collide with Earth, while the other asteroids were not disrupted from their orbits (and the CI chondrites are further out), or alternatively, if the entire asteroid belt was disrupted, why were we not struck predominantly by the predominant silicaceous bodies? Then, previous work by Drake and Righter (Nature 416: 39) showed that, based on isotopes of other elements, no asteroidal body could have delivered Earth's volatiles, and the problem becomes much worse if the predominant asteroids devoid of volatiles also struck Earth. Oxygen isotopes alone characterize both the Earth and the Moon as being different from all other bodies for which data are available.
There is a further problem: why do we think that the D/H ratio on Earth is primeval? On Mars, and particularly on Venus, D enrichment must have occurred, so why did it not occur here? Genda and Ikoma (Icarus 194: 42) showed that there should have been an enhancement of between 2-9 times on Earth; nine times would mean that the current Earth's hydrogen was originally of nebular composition.
The problem with this paper is that conclusions were drawn from a very minor subset of available data, it focused on isotope ratios of hydrogen for water but ignored oxygen, which are known to be characteristic, and worse, the conclusion was reached based on the premise that the set of possible source of water was {comets, asteroids}. The real set is {comets, asteroids, accretion disk}. Just because the current paradigm ignores the accretion disk as the answer does not mean it was not the source. Finally, in my opinion it is extremely wrong to reach a conclusion based on genuinely good analytical data, and then ignore all the previous papers that call the conclusion into question. If referees have any function at all, surely this is one of them?
Accordingly, I ignored it in my claim because it was too complicated to show why in a blog. The chapter in the ebook that dealt with this issue took over 11,000 words, and that assumed that some material from previous chapters had been read. In short, this paper would not have changed that chapter, so as far as I am concerned, the conclusions of the chapter stand.
Posted by Ian Miller on Oct 6, 2012 3:35 AM BST
I believe that society has now become addicted to technology, and accordingly as some of the adverse consequences come to the fore, such as resource depletion, we shall have to address them through science. We cannot just get off the horse and return to a preindustrial lifestyle because there are too many mouths to feed, and too many of these concentrated in cities. To do that, I think we need a greater proportion of the general population to understand how science works. Since I have now essentially retired from lab work, my approach to helping in this has been to publish fiction, with science in the background, and to support that, I have also started a literary blog. My last posting to that involved an answer to the question, why is the science behind invisibility relevant to you? The idea was to show how science does not work with facts, but rather uses them to develop further understanding. Whether I succeeded is a matter of opinion, but more important to me is whether what I wrote is suitable. I am not a teacher, a deficiency that may make what I wrote inappropriate. So, I am reposting that blog below, and I am interested in comments. Also, I rather fancy that many scientists themselves will not have realized the significance of the conclusion. So:
Why put something scientific into a story? If it is merely to impress, in my opinion the effort is wasted. Putting in something necessary to make the story work is much better, however in my writing I would also like to show something about the scientific approach. I feel rather strongly about this latter purpose because we now have so much dependence on technology that we are beginning to create new problems arising from it (such as the dependency on oil, which must run out sooner or later) so we need to know how to address them. An important point about science is that collecting facts and doing mathematics are not the goals; rather the goals are to understand, and to make use of that understanding. Now, let’s reconsider The Invisible Man. In my previous blog, I asked the question, can you think of anything very important relating to invisibility that is relevant to your life? My guess is that most people would shake their heads in despair at that question. How can invisibility have practical use? You simply cannot make people invisible.
The scientific approach looks at problems in a different way. The most common way is to ask and attempt to answer questions. So, why do we see things? Light comes from somewhere, strikes the surface of the object, and is reflected. We then ask, why is it reflected? Because the surface represents a change of refractive index. In The Invisible Man, Griffin became invisible by changing the refractive index of his body to that of air. Assuming that could be done, Griffin would truly be invisible, although there is a subtle price.
Changing a refractive index of an object is generally speaking impossible, but it is possible to immerse it in a medium with the same refractive index, in which case it will disappear, provided it is transparent. So now we ask, what is the difference between transparent and opaque objects? The answer is that opaque things have lots of internal surfaces (such as fractures between crystals) where light is reflected or scattered. We now see the price for Griffin: separate cells have surfaces, which perforce define changes of refractive index, so for Griffin to be invisible, he had to have no cells! That would make life somewhat difficult to maintain. Anyway, now we see we can make transparent objects become invisible by immersing them in a suitable fluid. That still leaves the question, why is this important for the average citizen? The answer is simple. Suppose you put a liquid on the surface of the skin that closely matches the refractive index of skin (about 1.5)? That makes all the roughness of the surface of the skin, which is quite effective at scattering light, invisible, which means that light passes deeper into the body. Now do you see the relevance? Think sunburn and skin cancer!
A number of oils have refractive indices around 1.47. Simply apply oils like coconut oil and you will baste in the sun! Get the skin wet with water (refractive index about 1.33) and your natural protection drops by about 50%. With close matching, very little reflection occurs. This becomes relevant when you apply sunscreens, because the carrying medium provides such matching, and removes almost all the natural reflectivity of the skin. The sunscreen, of course, stops the UV radiation while it is working, but if your sunscreen does not offer UVA protection, putting such screen on your skin may stop you burning, but it may pump the UVA into the lower dermis. Also, while a very high SPF may offer prolonged protection against UVB (which burns) the UVA screen usually decays more quickly. The SPF says nothing about UVA protection, and UVA is presumed to be capable of inducing a cancer. The remedy, of course, is to re-apply frequently, and I also recommend not rubbing it in, but merely smoothly spreading it and letting it dry.
The point I am trying to make is that a little bit of scientific reasoning, together with some necessary information, can lead to a much improved lifestyle. In my opinion, inserting some of these facts into stories, and showing how the reasoning works, is of some value. What do you think? In the meantime, next week I shall provide the answer to the other question that seems to be somewhat troublesome.
Now, is that appropriate? Let me know. Also, did you realize that the carriers in sunscreens by themselves actually promote sunburn and cancer?
Posted by Ian Miller on Sep 29, 2012 12:41 AM BST
In a previous blog, I discussed the case of whether platinum, palladium or gold could form oxo compounds. The argument that they could was published, with mountains of data that allegedly supported the case. Eventually, these assignments were found to be wrong, and one critic blamed the referees for permitting the original publication. Throughout the discussion, however, nobody seemed to come to grips with the problem: what comprises proof? One question that fascinates me is why do undergraduate science courses inevitably omit to address this question? Why do no such courses include the prerequisite for some, even brief, course in logic?
We sometimes see the argument, often attributed to Popper, that you cannot prove a statement in science; all you can do is falsify it. I think that is unnecessarily restrictive. One answer was given by Conan Doyle: when all possible explanations but one for an observation are eliminated, then that one, however unlikely it might seem, must be the truth. The reason why Popper's argument fails in such cases is that there was an observed effect, and therefore something must have caused it.
Set theory provides a formal means of answering the title question. Suppose I carry out some operation that addresses a scientific question and I obtain an observation, and to simplify the discussion, assume I am trying to obtain a structure of a molecule. There will be a set of structures consistent with that observation. Suppose I do another; there will be a further set of structures consistent with it. Suppose we keep making observations. If so, we generate a number of such sets, and because the molecule remains constant, the desired structure must be a member of the intersection of all such sets. The structure is proved when such an intersection contains only one element. Of course, this raises the question of the suitability of data. Simply reproducing the same sort of observation many times merely produces much the same set many times.
The problem, of course, is to ensure that the sets of structures that might give rise to the observation is complete because the logic fails when the truth was not considered, and proof fails when the sets are incomplete. (The truth not being considered may show up if the intersection of all sets is the empty set.) We may now guess at a problem with the oxo compounds: there was an awful lot of data consistent with the argued structure, but it was not definitive. This is one place where it is possible that the referees failed, but then the question arises, is it reasonable to expect the referees to pick it? Referees have general expertise, but only the author really knows what was observed. Should authors have to outline their logic? I think so, but I know I am in a minority.
I should also declare an interest in that last comment. I published a series of papers devoted to determining the substitution patterns on red algal polysaccharides, and I followed that logic. Accordingly, the papers tended to have a large number of set relationships, and a number of matrices. Rather interestingly, eventually the editor told me to desist and write papers that looked like everybody else's. Since I am not paid to write papers, and they made no difference whatsoever to my well-being, I simply desisted.
Posted by Ian Miller on Sep 23, 2012 12:53 AM BST
Yes, this is definitely off the formal topic, but I am curious to see what comes up. Most people have heard of the C. P. Snow inspired debate relating to the arts versus science, with which, as an aside, I disagree. I have a number of scientist friends who actively participate in some form of "art", usually music, and most scientists at least read something other than scientific papers and news items. On the other hand, I am not so sure that non-scientists understand the concepts of science, which I believe is bad because some decisions are coming that will strongly affect our future, and they will depend on science to get a good outcome. I am not suggesting that everybody study science, but I think it would be helpful if they understood enough of the underlying methodology to be able to tell the difference between a reasoned argument and snake oil. The resolution of reasoned arguments can be left to experts, but the ordinary person has to be able to tell which statements are reasoned and which are not if democracy is to work. If you are going to demand the right to vote, you have the obligation to vote in a reasoned fashion.
In this context, you might note that Plato was strongly against democracy. In "The Republic" he posed this question: if you are in a boat at sea with very limited supplies, do you want a vote or do you want a navigator?
Anyway, on the basis that if you believe something you should do something about it, I have self-published a couple of futuristic novels involving the concept of science in literature to get people thinking, and to support these I have started a second blog ( and I am starting with the theme science in literature. I have also posted a quiz question, which readers here might like to try their luck with. The question: can you think of a famous story involving a cloaking device that underpins a plot involving abuse of power, pride, wishing for what you should not have, and the curse of chattering women? If so, let me know and award yourself an imaginary chocolate fish. The one I am thinking of is extremely well-known, although probably very few have actually read it, which is something of a pity.
The second question is, can chemists come up with an answer sooner than those associated with books?
Posted by Ian Miller on Sep 14, 2012 4:54 AM BST
My alternative theory survived August! I found no papers that falsified the major premises, although one paper would have led me to change slightly what I wrote. The good news is that it far more strongly falsifies the standard position. This paper (Hirschmann et al., Earth Planet. Sci. Lett. 3465-348: 38-48.) demonstrated that molecular hydrogen is significantly more soluble in molten silicates when under pressure than had previously been realized. The standard theory is that early silicates were oxidized, the logic being:
(a) Modern volcanoes emit oxidized gases.
(b) Modern and ancient volcanic silicates have a similar composition.
(c) Therefore, ancient volcanic gases were oxidized (CO2 and N2)
My argument is that (c) does not follow. The “oxidation state” is not a valid variable (it is conserved in a closed system) and that the nature of silicates is determined by the free energy and depends on the local temperature and pressure, and on the movement of matter between phases. In this context, the major silicates in volcanic rock are olivines and pyroxenes, with the iron being present in the ferrous state. At much higher pressures (deeper) ferrous silicates disproportionate into ferric and iron, and so such cations in a rock do not indicate much except the local conditions when the rock crystallized.
The significance of this lies in the nature of the original atmosphere. Standard theory says “oxidized gases”; my argument was some reduced gases, which were generated when carbonaceous material (see my previous blog, “Carbonaceous Mars”) reacted with water thus producing CO and H2 (syngas) and when iron reacted with water to make ferrous or, if deep enough, ferric hydroxide and hydrogen gas. The hydrogen is critical for making some of the molecules that are critical for biogenesis, and to some extent these would be more difficult to make if hydrogen escaped rapidly to space. Evidence that hydrogen would dissolve in silicates meant that it would be available for further synthesis for a longer time. Magma can take a Gy to move 1000 km upwards.
This does not mean that my argument must be right, but at least it makes it more plausible, in which case the production of the precursors to life is not an extraordinarily unlikely event at all, but is probable on any Earth-like planet (Earth-like being defined as being of comparable size and having massive granitic cratons). What is “comparable”? The range of sizes is unclear, and this makes Mars a fascinating exploration site. Will Curiosity find clues to biogenetic material? We do not know yet; if there is any remaining on Mars it has to be protected from the ionizing radiation, so it will have to be buried. Digging is a problem, because digging has to be in the correct place and be deep enough. We await results.
Posted by Ian Miller on Sep 4, 2012 12:50 AM BST
While most scientists have mixed feelings about referees, particularly after having had a paper rejected, they also have mixed feelings about expressing views on refereeing. Once you get old enough, mixed feelings crystallize! This blog was inspired by p9, Chemistry World, August 2012. While "standard wisdom" asserted platinum, palladium and gold did not form oxo compounds, between 2004 and 2007 Craig Hill published papers containing a large amount of data supporting the claim that they did. These papers were subsequently retracted in light of further evidence. There was no question that the original data were correct, but the author now admits the interpretation of their significance was incorrect. The original authors stated that this showed science was working. "Not very well," answered one scathing critic, who stated the papers should have been stopped by the referees, and he was quite scathing about the quality of the refereeing. The issue is, is that opinion valid?
In my opinion, referees should never stop publication of a paper on the grounds that it is wrong unless they can show where, and give the author a chance to rebut their criticism. Science is in a bad way if papers can be rejected simply because referees do not believe them. If one learns nothing else from history, surely one should learn from the Almagest that authority has no place in science; only observations determine whether a theory is false. At stake is the future of science. Whatever science needs now, "priestly authority" is not one of them.
What I find to be of particular importance is that if the evidence was not sufficient, or it permitted alternative explanations, why did the critic not see this at some time during the following 8 years? If nobody can tell that something is wrong over 8 years, I think it is unfair to criticize the referee, who had a few days to view the paper, and furthermore, while he would have some general relevant experience, he would not be an expert in those specific areas. Whoever was at fault here (if anyone was) it was not the referees.
What could have gone wrong? The most obvious is that while a wealth of data was collected, it did not lead to a singular conclusion. I shall elaborate on this in a future post, because I have attempted to advocate a procedure for such structural analysis that is a little different from what many follow. The other problem is more serious, and that is, perhaps there is no place where doubts can be put forward and debated in a logical fashion. In these days of unlimited web space, this is correctable. It seems to me there should be such a forum, managed, and reviewed before postings are accepted, but reviewed for one purpose only: to ensure that the posting makes a legitimate point and is done so in accord with the logic rules of debate, i.e. as laid down by Aristotle, such as attacks on the conclusion are valid, but attacks on the person are not and resorting to authority are not.
Posted by Ian Miller on Aug 28, 2012 9:24 PM BST
During world war II, Germany made a certain amount of synthetic fuel by hydrogenating coal (the Bergius process). If one can hydrogenate coal, why not biomass? If we do not have an immediate answer, why not, and what are we prepared to do about it?
In fact there appears to be no good reason why we cannot because it has been done, at least to the workshop level. One process advocated during the previous energy crisis (Kaufman et al., Chemie Ing. Techn. 46, (1974) 14) involved taking finely divided biomass slurried in oil and mixed with nickel hydroxide and heating this to between 400 – 450 degrees C, with at least 5 MPa pressure for about twenty minutes, and in the presence of hydrogen, in which case it makes an oil that has immediate physical properties similar to diesel.
The advantage of this process is that all the biomass is useful, as any carbonaceous material can be hydrogenated and the products, essentially hydrocarbons, fit directly into the oil distribution system. The diesel and jet fuel cuts could probably be used directly, although some form of cracking would be required for petrol. Admittedly, a limited number of nitrogen heterocycles, where the nitrogen is at a position where aromatic rings are fused together are difficult to hydrogenate, but these should not be a problem for most biomass. An important point is the lignin, which contains a high proportion of the energy of the biomass, should hydrogenate smoothly. The yields of useful material obtained from a 50 kg/day unit were impressive, from memory in the low forty per cent range by weight, assuming oven-dried starting material. This included a small amount of pitch-like material made, which might be rehydrogenated, or alternatively used as a bitumen substitute.
So, why is this process almost never advocated? One reason might be that the production of hydrogen could be a problem. Another could be that it is unlikely that this type of process could be protected by patent, although the same is probably true for most oil refining technology. More likely reasons include this work has been essentially forgotten, and that high pressure chemistry is not fashionable. That raises the question, should the future be determined by our reluctance to work on what had been developed previously, our reluctance to visit the literature, or our fashion preferences?
Posted by Ian Miller on Aug 14, 2012 10:57 PM BST
July was a good month for my planetary formation theory. Of eleven meteorites known to have originated from Mars, one of which is approximately 4 Gy old, ten of them had carbonaceous material embedded in their basalts (Steele et al., Science 337: 212). My theory requires that carbon on the rocky planets had to be accreted as solids (carbon, carbides or carbonaceous material) and the atmospheres arise through this material becoming oxidised by water when temperatures of the rock get above about six hundred degrees centigrade. This will give rise to a mixture of carbon dioxide and methane, the extreme pressures causing carbon monoxide to largely further react. I argue that due to the expected chemical isotope effect during this oxidation, this reaction is the source of a significant contribution to the deuterium enhancement on planets, especially Venus but to a lesser extent on Mars. I also argue the reason Venus has almost no water is in part because it accreted at a higher temperature so it accreted less, and because it has more carbon, it used most of its water making its oppressive atmosphere, thus amplifying the chemical isotope effect.
In my ebook I made over 80 predictions, but I never had the nerve to predict that Martian basalts would contain carbonaceous material, although I did predict this for Mercury. There were two reasons. The first was that I expected the surface of Mars would be too oxidised, and little carbon could remain. The second was that I was aware of the meteorites, I knew that no carbonaceous material had been reported, and it never occurred to me that the reason why not was that nobody had looked!
While on the subject of primordial atmospheres, standard theory requires that reduced nitrogen arose from oxidation of atmospheric nitrogen, with nitrous and nitric acids subsequently being dissolved in the acidic seawater and then being reduced. Nitrites are reduced at about 70 degrees C over pyrites, nitrates at about 120 degrees, and of course it is usually argued that this would happen at black smokers. My argument was that nitrous acid is not good to have in the presence of the amines needed for life as it would diazotize them, but I also learned (Heilman et al. JACS 134: 11573) that nitrosyl compounds act as a source of NO, which in turn is a powerful antibiotic, which is hardly the most desirable environment for bacteria to try evolving. (If the atmosphere was primarily carbon dioxide, the ancient seas would be rich in ferrous ions from weathered basalts, and hence nitrosyl compounds should form.) The antibiotic properties of NO have been known for some time; it was just that (blush) I did not know it.
Posted by Ian Miller on Aug 5, 2012 12:35 AM BST
In the July edition of Chemistry World there was an item (p 20) on the SN2 reaction involving ballistic experiments on the reaction between hydroxide (with or without additional water molecules) and methyl iodide in helium. The results appeared to be that hydroxide plus methyl iodide by themselves simply led to ballistic outcomes. If one molecule of water could be incorporated, the iodide left on the trajectory consistent with the classic textbook SN2 result. If two molecules of water were incorporated, a longer-lived complex was formed that had a lifetime sufficiently long that the iodide could come out at any direction. That is unexceptional. However, the item ends with a statement: “the SN2 mechanism that undergrads are told is a fairy tale, up there with Santa Claus and the Easter bunny”. The commentator was surprised that any of the results supported the textbook version. So it appears that in volume 1 of my Elements of Theory, I joined the Easter bunny. Oh dear!
What can my defence possibly be? First,  I discussed the SN2 mechanism in an example of where science had not fired properly, in this case the so-called non-classical 2-norbornyl cation. In the 2-norbornyl system, leaving groups that are endo react second order to give exo products, which is the textbook SN2 reaction. However, exo leaving groups react significantly faster and give exo products, which shows that reaction is not simple SN2. There are clear reasons why the SN2 mechanism is unlikely to apply to these exo substituted molecules and the chapter pointed out that despite the extreme amount of work carried out on the 2-norbornyl system, the reason for the acceleration of the exo substituents remained unexplained. (The book has over seventy problems at the end; one was to find an explanation for the so-called non-classical ion, so for those who want an intellectual exercise, why not try your luck? As a clue, my answer relies on each side being partly correct, and each side correctly falsifying the other side in some respects. Given two Nobel prize-winners failed to reach a  conclusion over ten years, I rate this as one of the more difficult problems that I set.)
So, at the risk of being hammered again as something worse than an Easter bunny, I wish to point out that the information on the given experiments are quite consistent with the textbooks as I know them. First, there is no evidence whatsoever that there was no structural inversion (difficult to show with methyl iodide). The concept that there may be a small energy minimum on the reaction coordinate is expected if a transition state is stabilized so that it lies between two energy maxima, and if such a longer-lived intermediate can exist, the Uncertainty Principle requires that it has rotational uncertainty, let alone classical rotational motion from the collision. Finally, classical Debye-Huckel theory predicts stabilization of ionic intermediates from adjacent water molecules. There was nothing I copuld see in these experiments that is not in accord with the textbooks.
Actually, I agree with the commentator that the textbook discussion of the SN2 mechanism is an oversimplification, however my criticisms lie outside the scope of these experiments. Perhaps the subject of another blog.
Posted by Ian Miller on Jul 26, 2012 12:59 AM BST
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