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  1. #1
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    Default New Molecule May Challenge Vibration Theory of Olfaction

    A new molecule, which I jokingly refer to as "Bigsly's Benzene", may present a serious challenge to Luca Turin's explanation of olfaction. You will recall that on a previous thread, Bigsly was rather frustrated that a molecule had yet not been devised to either prove or disprove Turin's theory once and for all. Well, it may have just happened, although we can't be positive quite yet. But one thing is certain - this molecule will likely present a serious challenge to Turin's theory. How his theory handles it could be a win for either side.

    You can read about the molecule here. The molecule, known as 1,2-dihydro-1,2-azaborine (abbreviated DHAB) is isoelectronic with the well-known aromatic compound benzene. Isoelectronic means that two things have the same number of electrons, although the exact configuration may differ. But often - and this is important - isoelectronic things can have almost exactly the same shape.

    Benzene is referred to as "aromatic" because compounds like it have distinctive odors. Benzaldehyde, vanillin, coumarin - the list goes on and on. But the thing that's important here, and which is mentioned in the article cited above (but not in the original scientific communication), is that the discoverers accidentally smelled the substance while analyzing it, and discovered that it smells like benzene! And not only that - if you look at another similar molecule called borazine, it, too, is said to have an "aromatic" smell.

    Importantly, all three of these substances have essentially identical shapes. And we know that all three smell at least similar, and at least two of them (benzene and DHAB) may smell the same. But even more importantly, these substances should not smell the same by Turin's theory, unless he can somehow show that they should be exceptions. The reason is a significant difference in the IR spectrum, which you can see in supplementary material here. If you look on page S17 of this supplementary material, you will see that the new molecule has a boron-hydrogen stretching frequency, which is due to a B-H bond in the molecule. Well, the thing about that is that Turin's theory attibutes the thiol-like (sulfurish, rotten egg) odor of boranes to this bond's vibration. Indeed, the fact that boranes (B-H) and thiols (S-H) smell similar is said to be due to the fact that these bonds have stretching freqencies at a nearly identical and somewhat unusual value. I had always considered this one of Turin's stronger pieces of evidence.

    So the bottom line is that the new molecule should stink like a thiol according to Turin's theory, and yet it doesn't - it smells like a molecule with exactly the same shape. In other words, we now have a borane with exactly the same shape as a non-borane, and yet they smell the same.

    It's important to put this in perspective. Another example which Turin has cited is deuterium-substituted acetophenone (acetophenone-d8) versus normal acetophenone. These molecules have almost the same shape and slightly different electronics, and apparently have either identical smells (when compared by another lab), or very slightly different smells (when compared by Turin). So in that case, two very similar substances give at best very similar results. But in the new case, a significant electronic difference in identically shaped molecules is NOT producing a difference in odor. And not only is there a significant difference in electronics - this difference is right across home plate in terms of Turin's theory. It is right where one of his core examples says a certain odor should be. If this substance had smelled like a thiol, then Turin could have claimed it as a victory. But the fact that it appears to smell like benzene is a significant reversal, in my opinion.

    Let me elaborate on the virtues of this example. From what the discoverers of DHAB have told us, this new isoelectronic analog of benzene has a remarkable number of electronic and chemical similarities to benzene. But one of the striking remaining differences is the presence of the B-H bond, and its effect on the IR spectrum. You almost could not have asked for a better example to test this question. This molecule truly is the answer to Bigsly's wish. Nevertheless, we must be cautious. We don't have a really good report on the odor of the compound yet. Perhaps the odor does have some thiol character. We should know more soon.

    Now it is possible that Turin could have an explanation. He already has several explanations for cases where things either smell or don't smell according to his theory. These reasons do make sense. But the problem is Occam's razor. Competing theories need say nothing other than that the molecules are the same shape and - lo and behold - they smell the same. That kind of simplicity wins hearts and minds. So unless Turin has a very, very tidy explanation for the discrepancy - and preferably one with some additional predictions - then things are going to get even rougher for vibration theories.

    I will finish with a quote from Turin himself, applied to his deuterated acetophenone example:

    In other words, two molecules with identical shapes and different vibrational spectra smell different.
    Well, those were both very small differences. Here, we have two molecules with identical shapes and significantly different vibrational spectra which apparently smell the same.

    I don't think this is over yet. In fact, the fight over this molecule may just be starting. But in my opinion, this is likely to be a big day for the "standard model" of olfaction.
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  2. #2

    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    OK, thanks for the news!
    Let`s wait till some explanations from the both sides
    Vetiver The Great!!!

  3. #3

    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    I love all these "science bits". I feel like I'm in an old L'Oreal advert. It's fascinating, I hope Turin has got an answer as to why!

  4. #4
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    You two are ahead of the curve. I've already heard from Luca, and am chomping at the bit to post what he told me. That's what's so fun about science - new data comes in and the landscape changes. It does seem that this "branch" of chemistry (the behavior and theory of "aromatic" systems) has provided quite a large part of the drama of chemistry since about the mid-1800's. I'm hoping that both sides will marshall their best arguments here, leaving lots of room for debate. So much more productive than fighting over Creed or Kouros, too! Stay tuned....
    Last edited by Redneck Perfumisto; 15th January 2009 at 12:10 PM. Reason: martial is a bit strong... we want a fight, but not that much :)
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  5. #5

    Somerville Metro Man's Avatar
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Guys I hate to rain on your parade but there are a number of inaccuracies in the basic treatise being put forward above.
    1.) "aromatic" compounds are so named because of their odor.
    This is the definition of chemical aromaticity and what a chemist means when he refers to an aromatic compound:
    Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. It can also be considered a manifestation of cyclic delocalization and of resonance.

    You will notice that nowhere in that definition does scent enter into it. I can tell you that there are many aromatic compounds that have little scent to them at all and really every organic chemical has a scent and therefore they should all be aromatic under the definition proposed above.

    2.) Boranes and Thiols smell similar.
    Simply and completely nonsense I work with both of these kinds of compounds and if you take any comporable borane and thiol they will, in no pair that I am aware of, come even close to smelling similar. To give perspective I have easily worked with over a 100 of each of these kinds of compounds and know what I am talking about and have smelled over my 24 years in the lab.

    3.) Using the IR frequency to make comparisons.
    If anyone you know has an Infrared emitter in their nose this analogy might hold true. That things have similar stretching frequencies when exposed to beam of infrared light has in no way been connected to the way things bind in a biochemical way. You knw what else shows an IR stretch of around 2550 cm-1?
    Alcohols do. Their stretch is more broad because they are better Hydrogen-bond donors but they also have the same IR frequency. Do you think they have the same nasty odor as thiols. Of course not!!
    This argument is just ridiculous and based on a foundation of nonsense.

    So much of what was written above is inaccurate that the whole hypothesis, which might have some merit I'll have to look at the paper, gets obscured in the inaccuracies.
    Last edited by Somerville Metro Man; 15th January 2009 at 12:12 PM.
    More writing on fragrance by me to be found at http://www.cafleurebon.com/

  6. #6
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Come, come, SMM. Of course I'm aware of point 1. I suppose I could have said they were historically named that way. Perhaps I should have been more explicit and a bit less journalistic. But are the peeps really ready for a digression into the validity of the Hückel approximation for these systems? I think not. Sorry, but I refuse to bring degenerate HOMOs into the discussion on a board like this (don't worry, folks - they're talking about electrons, not us).

    Point 2 is good. I would really like to see Turin address that whole issue of boranes and thiols in a very concrete fashion with a wide variety of compounds from the two classes. Clearly we don't expect functional analogs to smell identical for rather basic reasons, and given the large number of receptor types, I would expect even minor differences to be magnified so greatly as to make things very nasty. Perhaps you scoff, but enquiring minds want to know. I do agree completely that the scale of similarity is a fundamental dilemma in the whole field. Thank God I'm only a bystander.

    Point 3. You do have an IR emitter in your nose. You have many of them. They're called cells. Sorry - couldn't resist. You are quite correct that "things have similar stretching frequencies when exposed to beam of infrared light has in no way been connected to the way things bind in a biochemical way". Exactly. That is what Turin is attempting to do. He's even using QM tunnelling, which almost everybody thinks is goofy. Well, one of my advisors didn't, and I still think that he's right about its involvement in the appearance of certain disproportionately small energetic barriers in certain non-alternant aromatics. But I digress again. Is it goofy? Perhaps. Apparently some folks were persuaded that it was worth doing the theory to see if a phenomenon which would, in principle, amount to a tunnelling IR spectroscope would be viable, and it was. Well, at least they say it was. Given that the T in STM doesn't stand for thiols, perhaps QM tunneling is real. Who knows. But I'm here to learn - even from other people's mistakes. Or my own.

    I don't know - I think I'm going to quit before I get really snarky. I once laughed at a snarky comment somebody else made about chaos theory at a conference on the theory of emerging aromatics, and a speaker got offended. I never got to talk to him. I still regret that one. The point is, yes, we know.

    Luca has given me permission to post his comments - I'll do so later. I've got to go to work. I'm sorry I'm bitchy, SMM, but I was really excited about this molecule, and you did rain on my parade a bit. But I know that your intention was good, as was mine.
    * * * *

  7. #7
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    I'll begin by apologizing for my pissy post. SMM didn't deserve that rude treatment. I'll deal with myself on that later, after a bit more reflection. Both he and BN deserved a much more thoughtful response than what I gave.

    I promised you Luca's response to my initial post, so here it is:

    Hi there !

    Very nice, but.... no cigar:

    In order to be perceived by an electron tunnelling spectroscope, the partial charges on the atoms have to be reasonably large. The borazine is by no means the only example: for example nitriles in cyanohydrins have no smell, and no IR intensity either ! Frar from being a disproof of IETS theories, this fact is a confirmation :-) Another example: while boranes smell of sulfur, carboranes do not, and the latter turn out to have nonpolar bonds with almost no partial charge on the B-H. This was discussed at length in Brookes et al's paper in Physical Review Letters 99, 238104 (2007) in the context of calulations of line intensities. I will calculate the wonderful new borazine and let you know what the charges look like.

    Luca


    He went on to note that he enjoys our discussions of olfaction. I hope that still holds true. In any case, he seems confiident that the new molecule's scent can be explained by his theory in its current state. Although I've seen the cited article, I think I'll look at it again, keeping the new molecule in mind. And if Luca chooses to report anything further to me, I'll gladly post it here for him.

    Added Note - Luca also said this about the partial charges:

    The partial charge thing gets pretty arcane because pc's arent measurable, etc. but the bottom line is uncharged atoms cannot be perceived by "IR" spectroscopes and we have no idea yet how much charge is needed before we can smell something.

    Which of course makes me extremely curious about what sort of series-type experiments might flush out that information.

    Again, my apologies to SMM and BN. I will take SMM's good advice to post in a more careful manner on these topics (provided that upon further reflection I still think it's a good idea to post on science here at all).

  8. #8
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Quote Originally Posted by Redneck Perfumisto View Post
    Again, my apologies to SMM and BN. I will take SMM's good advice to post in a more careful manner on these topics (provided that upon further reflection I still think it's a good idea to post on science here at all).
    I didn't have a problem with the tone of any of your posts (of course, I wasn't the target). Nothing wrong with a little snarkiness to make the debate more interesting.

    As for posting on science, this site doesn't have enough of it! To me, the most interesting threads are the ones that deal with actual research and evidence as opposed to someone's feelings or opinions. It's nice to actually learn something now and then. I say, bring it on, RP!
    Marge: Do you want your son to become Chief Justice of the Supreme Court or a sleazy male stripper?
    Homer: Can't he be both, like the late Earl Warren?



  9. #9

    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Love to read this. I'm scraping at biochemistry cobwebs in my brain.
    2 questions..
    I thought Aromatic compounds, in biochemistry, contained a typical carbon ring. Versus the other definition of aromatic??
    If the researchers sniffed DHAB and it smelled similar to benzene, well that doesn't mean it smells IDENTICAL to benzene, does it? Is there any way to measure if something smells identical to something else? (I guess that's 3 questions).
    Thanks for any explanation. (Lay that hard science on me! Wooohooo!)
    P.S. I think I need to read Luca's book now. It's sitting on my dresser. It will make a nice change from the 'Twilight' series that I've been devouring at my daughter's behest!

  10. #10
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    OK, dpak. Will do - but a bit more carefully. Somerville and I have talked about this offline with Turin. SMM has a very interesting combination of extensive factual knowledge of boron chemistry as well as being a nose (if I can toot his horn a bit - he has more practical experience with boron compounds than any chemist I've ever known personally). I would absolutely love to hear his impressions of this substance versus a variety of other boron/nitrogen compounds, and most particularly benzene itself. Some people believe in the virtue of untrained noses as test subjects, but I believe that trained noses may have greater powers of differentiation.

    Quote Originally Posted by lizzie_j View Post
    Love to read this. I'm scraping at biochemistry cobwebs in my brain.
    2 questions..
    I thought Aromatic compounds, in biochemistry, contained a typical carbon ring. Versus the other definition of aromatic??
    The whole confusion was due to my simplistic post. Aromaticity was what I worked on back in the day. It has been an evolving definition since its historical beginning in the 1800's. The original grouping of certain odorous substances together was resonsible for the name (the view of one professor of mine - that view asserts more than what you'll see on wikipedia), but it quickly expanded to include certain specialized chemical behaviors (unique reactions, unexpected stability, low saturation) that the compounds showed. As the atomic theories gained power, people figured out that the common thread was precisely what you say - the fully unsaturated 6-membered ring, with benzene being the prototype. But certain things were anomalous, and explaining those phenomena over more than a century, in more and more sophisticated ways, is what the field is all about. SMM nicely summarized those points. The modern definitions center around the idea of cyclic delocalization of electrons, with the primary manifestation being an extra stabilization of the molecule as a whole, but also including magnetic effects which are extremely diagnostic for the condition, as well as its antithesis, antiaromaticity - a destabilizing or non-stabilizing condition where the molecule essentially rebels against the "sharing" of electrons by delocalization. The simplest and most profound explanation (in my opinion) was due to Hückel in the 1930's. Put simply, he applied quantum theory to the system and reduced the complexity of the problem by simplifying assumptions until it was so bare-bones as to almost reduce to symmetry arguments and ratios of integers alone (which are still used to solve the problems, incidentally). But by his method it's readily seen that certain geometric arrangements of atoms (e.g., unsaturated 6-membered rings, as well as 10, 14, 18, etc.) are stabilized and others (4, 8, 12, 16, etc.) are destabilized, in extraordinary agreement with experiment. The whole idea has been extended much further, and led to other huge advances such as the idea of orbital symmetry conservation in certain organic reactions.

    But everybody should note - the modern olfactory definition of "aromatic" (sage, rosemary, etc.) is not to my knowledge related to the original group of substances which gave rise to the compound class. That evolution is probably an excellent history-of-chemistry question. I'll see if I can find my old notes from the class I took, which covered the late 1800's and early 1900's.

    Quote Originally Posted by lizzie_j View Post
    If the researchers sniffed DHAB and it smelled similar to benzene, well that doesn't mean it smells IDENTICAL to benzene, does it?
    Absolutely right - it does not. All we have at this point is something reported by a journalist in a non-peer-reviewed article, although I will say that C&EN is - in my opinion - a far more reliable reference than "personal communication" or "work in progress"! The term they used was "smells like benzene". Now I may be reading a lot into this, but benzene has a pretty distinctive smell that most chemists are familiar with. Add a single methyl group and you've got toluene, and most every chemist knows that smell, too, and if it smelled like toluene, they would likely have said that, although we can't be sure. But the important point is that it very likely smells much closer to benzene than to a thiol, or pyridine (benzene with a nitrogen replacement), or other common organics to which it might have been likened. Nevertheless, you're right - we don't know exactly how similar. And similarity is a gruelingly hard thing to describe, in my opinion, without getting some better, harder numbers into the mix.

    Quote Originally Posted by lizzie_j View Post
    Is there any way to measure if something smells identical to something else? (I guess that's 3 questions).
    It's not my field, but I'll try to answer from what I've read and my opinion based on that. Yes - if not in practice at the moment, then in principle soon. It's much like the rest of biochemistry. In vivo, ex vivo, and receptors. Of course there are humans, but it helps to use more than single individuals there, and it has the same weaknesses as other animal tests. I've also seen some very interesting studies using insects, or isolated olfactory workings. But the most interesting to me are olfactory receptors. See for example: Chem. Senses 33: 639–653, 2008 (doi:10.1093/chemse/bjn032). The title of that article is "Relationships Between Molecular Structure and Perceived Odor Quality of Ligands for a Human Olfactory Receptor". We know that this has to be the future, based on what happened with drugs. I'm confident that one day we'll be able to have a beautiful quantitative fingerprint for substances against some standard array of olfactory receptors, and it will be as good or better than a human nose, and more reliable. Just my opinion, but that's what I think. I don't exactly have to put on the Carnac hat to foretell that one.

    Quote Originally Posted by lizzie_j View Post
    Thanks for any explanation. (Lay that hard science on me! Wooohooo!)
    That's the spirit! I love it when people here lay the hard art on me, too, because that's what I need! You can probably tell that I'm not well-rounded.

    Quote Originally Posted by lizzie_j View Post
    P.S. I think I need to read Luca's book now. It's sitting on my dresser. It will make a nice change from the 'Twilight' series that I've been devouring at my daughter's behest!
    Yes, I need to do some reading, too. I'm particularly interested in the theory of what amounts to a molecular IR spectroscope. Even if this isn't how nature does it (and I am keeping an open mind on that), there is no law preventing humans from doing it. Except perhaps the law that if you can't build a weapon with it or a convincing case for a fast medical application, it won't get funded. Perhaps they could make it shiny and white and put an apple on it.

    My son has been trying to get me to explain to him why girls love "Twilight". I haven't looked into it, but my off-the-cuff guess was that it was the same thing as Romeo and Juliet - the longing of a beautiful but forbidden love. If you or somebody else knows the answer to that, I won't consider it OT in the slightest!!!
    Last edited by Redneck Perfumisto; 17th January 2009 at 10:47 AM. Reason: precisedly
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  11. #11

    Somerville Metro Man's Avatar
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Quote Originally Posted by Redneck Perfumisto View Post
    Absolutely right - it does not. All we have at this point is something reported by a journalist in a non-peer-reviewed article, although I will say that C&EN is - in my opinion - a far more reliable reference than "personal communication" or "work in progress"! The term they used was "smells like benzene". Now I may be reading a lot into this, but benzene has a pretty distinctive smell that most chemists are familiar with. Add a single methyl group and you've got toluene, and most every chemist knows that smell, too, and if it smelled like toluene, they would likely have said that, although we can't be sure. But the important point is that it very likely smells much closer to benzene than to a thiol, or pyridine (benzene with a nitrogen replacement), or other common organics to which it might have been likened. Nevertheless, you're right - we don't know exactly how similar. And similarity is a gruelingly hard thing to describe, in my opinion, without getting some better, harder numbers into the mix.



    It's not my field, but I'll try to answer from what I've read and my opinion based on that. Yes - if not in practice at the moment, then in principle soon. It's much like the rest of biochemistry. In vivo, ex vivo, and receptors. Of course there are humans, but it helps to use more than single individuals there, and it has the same weaknesses as other animal tests. I've also seen some very interesting studies using insects, or isolated olfactory workings. But the most interesting to me are olfactory receptors. See for example: Chem. Senses 33: 639–653, 2008 (doi:10.1093/chemse/bjn032). The title of that article is "Relationships Between Molecular Structure and Perceived Odor Quality of Ligands for a Human Olfactory Receptor". We know that this has to be the future, based on what happened with drugs. I'm confident that one day we'll be able to have a beautiful quantitative fingerprint for substances against some standard array of olfactory receptors, and it will be as good or better than a human nose, and more reliable. Just my opinion, but that's what I think. I don't exactly have to put on the Carnac hat to foretell that one.




    Yes, I need to do some reading, too. I'm particularly interested in the theory of what amounts to a molecular IR spectroscope. Even if this isn't how nature does it (and I am keeping an open mind on that), there is no law preventing humans from doing it. Except perhaps the law that if you can't build a weapon with it or a convincing case for a fast medical application, it won't get funded. Perhaps they could make it shiny and white and put an apple on it.
    Some additional comments to illuminate some of the points RP just made.
    Benzene has a very distinctive smell and he is right every chemist who has ever been in a lab setting will recognize it. Therefore when a researcher says it smells like benzene they probably have apretty good basis to compare. As also stated that is not scientific proof that is what we call anecdotal evidence and we strive for more quantifiable means usually. On the other hand this anecdotal evidence can sometimes be the forerunner of the harder data. A personal example was in graduate school my project was to synthesize one of the components of natural grapefruit oil. On the day that I performed the last step of the synthesis i smelled the flask and sure enough it smelled like the rind of a grapefruit. At that point I reported to my advisor the anecdotal evidence based on the smell of grapefruit in my flask that I was done. My advisor told me to go measure the spectral properties and then I would be done after I had physical data to back up my nose. For this research, which is not centered on scent, that it smells like benzene makes for an interesting inital read on its eventual importance.
    Further the difference in smells. While I can't describe Benzene's smell so well I can give you two very real world similarities to compounds that RP mentioned above. Toluene smells similar to model airplane glue. Thiols are what a skunk produces when it sprays. You can imagine that neither of those smells would be mistaken for anything else. The theory as it is proposed is that boranes should smell more similar to skunks than to airplane glue. My experience with boranes tells me that there is a wide spectrum of odors to them and it is not so far-fetched for a borane to smell like bezene.
    As to the quantifying of what things smell like I think you are going to have to use the power of statistics here and you would have to screen a number of smells across a wide variety of subjects. We already know other senses sight, hearing, taste are extremely variable from person to person it would seem unlikely that smell is also not the same. Heck what we chalk up to skin chemistry might just be the way we all differ in perceiving smells. Anosmia is a known phenomena just as astigmatism and color blindness making all of this more difficult when delving into the realm of the senses.
    One experiment I am surprised Luca Turin has not tried is comparing the deuterated solvents used in NMR spectroscopy. There he has pairs of things like acetone and its deuterated form. Acetone is nail polish remover so it has a distinct smell. There is also dimethyl sulfoxide, or abbreviated DMSO, and its completely deuterated form. DMSO has a distinct garlic-like odor to it. There is also deuterated chloroform and methanol where all of the hydrogens are replaced with deuterium. Chloroform and methanol have slighter fragrances to them but they should be detectable to a sensitive nose. There is even benzene and deuterated benzene.
    Finally I'm not sure where I come down on the biological IR emitter. For now I think I'll also do some more reading before saying too much.

    My comment on the "Twilight" series is if you have a Y chromosome you are not interested.
    Why is that? Soetimes those of us with a Y chromosome are just lucky.
    Comparisons to "Romeo and Juliet" should absolutely stop at star-crossed lovers and go no further.
    Last edited by Somerville Metro Man; 17th January 2009 at 01:57 PM.
    More writing on fragrance by me to be found at http://www.cafleurebon.com/

  12. #12

    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Quit OT answer about the Twilight thing: It's got: Teens, outsiders who feel like they will never fit in, forbidden love that conquers all--even mortal danger, pretty girl who is not well described and could be ANY brown haired teenage girl gets drop dead gorgeous guy because she smells so good he can barely resist 'biting' her (her scent appeals to him as if she were his personal heroin), relatively chaste love (no sex, so I assume parents the world over approve of series for this reason), boyfriend is very wealthy and can buy girl anything, competition boyfriend is also drop dead gorgeous (and a werewolf). Just a few of the points that might appeal to the romantic side (is there any other side?) of a teenage girl.

    Back on topic..thanks both to you and SMM for the elaborations/explanations. Much appreciated!

  13. #13

    purplebird7's Avatar
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Thanks for this post, Redneck.
    I just answered another thread where a person asked questions about olfactory theories.
    http://community.basenotes.net/showthread.php?t=222025
    (I only speak in layman's terms, though!)
    And I referred that person to this thread for an update.
    Last edited by purplebird7; 18th January 2009 at 02:01 AM.

  14. #14

    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    My son has been trying to get me to explain to him why girls love "Twilight". I haven't looked into it, but my off-the-cuff guess was that it was the same thing as Romeo and Juliet - the longing of a beautiful but forbidden love. If you or somebody else knows the answer to that, I won't consider it OT in the slightest!!!
    http://www.theatlantic.com/doc/200812/twilight-vampires
    All these moments will be lost in time, like tears in rain.

  15. #15
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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Quote Originally Posted by Somerville Metro Man View Post
    Some additional comments to illuminate some of the points RP just made.
    Benzene has a very distinctive smell and he is right every chemist who has ever been in a lab setting will recognize it. Therefore when a researcher says it smells like benzene they probably have apretty good basis to compare. As also stated that is not scientific proof that is what we call anecdotal evidence and we strive for more quantifiable means usually. On the other hand this anecdotal evidence can sometimes be the forerunner of the harder data. .
    Well said. Anecdotal evidence tends to be where we get hunches and suspicions. In my opinion, a scientist should take hope and courage from the anecdotal, but should immediately look for the strongest possible rigorous tests to disprove it, and should not rest until attacks upon one's own position are a waste of time.

    Quote Originally Posted by Somerville Metro Man View Post
    A personal example was in graduate school my project was to synthesize one of the components of natural grapefruit oil. On the day that I performed the last step of the synthesis i smelled the flask and sure enough it smelled like the rind of a grapefruit. At that point I reported to my advisor the anecdotal evidence based on the smell of grapefruit in my flask that I was done. My advisor told me to go measure the spectral properties and then I would be done after I had physical data to back up my nose. For this research, which is not centered on scent, that it smells like benzene makes for an interesting inital read on its eventual importance..
    I love your example. I think every chemist should have one of these experiences. But yours was olfactory - the best one possible, in my opinion. In my case, it was a strange and beautiful color that disappeared before I could prove what it was. I "knew" I had my substance - and then spent years proving it.

    Quote Originally Posted by Somerville Metro Man View Post
    Further the difference in smells. While I can't describe Benzene's smell so well I can give you two very real world similarities to compounds that RP mentioned above. Toluene smells similar to model airplane glue. Thiols are what a skunk produces when it sprays. You can imagine that neither of those smells would be mistaken for anything else. The theory as it is proposed is that boranes should smell more similar to skunks than to airplane glue. My experience with boranes tells me that there is a wide spectrum of odors to them and it is not so far-fetched for a borane to smell like bezene..
    Nice summarization. The data reported by the people who synthesized the new molecule back up the idea that this molecule is like benzene in many ways. There is also anecdotal olfactory similarity. My initial thought was that this similarity, if validated, might prove difficult for Turin's theory. Turin says that on the contrary, one of his previous explanations for problematic molecules works here as well. It will be extremely interesting for me to see how tidy his explanation is. New data points always bring the possibility of better or worse explanation.

    The fact that Somerville thinks this smell ("like benzene") is reasonable for a borane is also anecdotal evidence, but it is the kind of evidence that I really want. Humans are wonderful pattern-matching machines, able to spot similarities in situations that the most sophisticated programs simply cannot keep up with. In real life, a scientist walks down the hall to an expert colleague: "Say, does this smell like a borane to you?"

    Quote Originally Posted by Somerville Metro Man View Post
    As to the quantifying of what things smell like I think you are going to have to use the power of statistics here and you would have to screen a number of smells across a wide variety of subjects. We already know other senses sight, hearing, taste are extremely variable from person to person it would seem unlikely that smell is also not the same. Heck what we chalk up to skin chemistry might just be the way we all differ in perceiving smells. Anosmia is a known phenomena just as astigmatism and color blindness making all of this more difficult when delving into the realm of the senses..
    As the man says, numbers is what he does! Statistics can even turn anecdotal evidence into the stuff that convinces skeptics.

    Quote Originally Posted by Somerville Metro Man View Post
    One experiment I am surprised Luca Turin has not tried is comparing the deuterated solvents used in NMR spectroscopy. There he has pairs of things like acetone and its deuterated form. Acetone is nail polish remover so it has a distinct smell. There is also dimethyl sulfoxide, or abbreviated DMSO, and its completely deuterated form. DMSO has a distinct garlic-like odor to it. There is also deuterated chloroform and methanol where all of the hydrogens are replaced with deuterium. Chloroform and methanol have slighter fragrances to them but they should be detectable to a sensitive nose. There is even benzene and deuterated benzene..
    I agree. There is one case I know of that seems to be a split decision - deuterated acetophenone (see info by Turin on isotopes and odor at the bottom of the page here). When in doubt, the answer is always more data! Massive testing of NMR solvents would be cheap, easy, and safe. No matter what, the answer would be interesting. And you're right - do a lot of them. Now that we know we're throwing stuff at a large number of receptor types, you would expect lots of variation according to almost any theory. But the more substances you do this with, the more likely that patterns will emerge.

    Quote Originally Posted by Somerville Metro Man View Post
    Finally I'm not sure where I come down on the biological IR emitter. For now I think I'll also do some more reading before saying too much..
    I agree - this needs close scrutiny. I was just joking about cells being emitters, too. If I understand Turin correctly, he is not actually testing vibrational states by any kind of normal IR emission/absorption, but rather is proposing that vibrational states in docked small-molecule and very-small-molecule odorants essentially act as energy shunts which couple to an electronic state transition or process when the receptor fires. In essence, the firing of the electronic process "senses" the vibrational states of the docked molecule in some fashion, thereby affecting the overall signal from the receptor over time. Technically you are correct, it is an emitter, in the sense that the odorant is left in a vibrationally excited state, but only in a sort of auxilliary way. I'm probably being a bit more vague than Turin, to allow his idea some wiggle room. There are a variety of ways in which I can imagine this happening, but the gist of it is that one might see a high degree of functional group detection in odorants by an interesting form of vibrationally coupled electodynamic discrimination rather than by steric and electrostatic discrimination alone.

    While I am not settled on the need for such a mechanism, is seems reasonable enough to warrant investigation. And because humans like to build their micromachines using moving electrons, I see this as a potential win/win situation, because if nature doesn't use this and it works, perhaps we could do some neat stuff with it.

    Quote Originally Posted by Somerville Metro Man View Post
    My comment on the "Twilight" series is if you have a Y chromosome you are not interested.
    Why is that? Soetimes those of us with a Y chromosome are just lucky.
    Comparisons to "Romeo and Juliet" should absolutely stop at star-crossed lovers and go no further.
    My wife was wondering why I was laughing so hard. Little does she know. I think no matter what's up with vibrations, you and my son are definitely on the same wavelength!
    * * * *

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    Default Re: New Molecule May Challenge Vibration Theory of Olfaction

    Quote Originally Posted by lizzie_j View Post
    Quit OT answer about the Twilight thing: It's got: Teens, outsiders who feel like they will never fit in, forbidden love that conquers all--even mortal danger, pretty girl who is not well described and could be ANY brown haired teenage girl gets drop dead gorgeous guy because she smells so good he can barely resist 'biting' her (her scent appeals to him as if she were his personal heroin), relatively chaste love (no sex, so I assume parents the world over approve of series for this reason), boyfriend is very wealthy and can buy girl anything, competition boyfriend is also drop dead gorgeous (and a werewolf). Just a few of the points that might appeal to the romantic side (is there any other side?) of a teenage girl.
    Do I detect two X chromosomes? OK, I'm starting to get it...

    And now I got it - thanks, David!

    The article is entitled "What Girls Want". Boys - it ain't Kouros.
    * * * *

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