[HN Gopher] Perfluorocubane is (as you would expect) weird
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Perfluorocubane is (as you would expect) weird
Author : kens
Score : 182 points
Date : 2022-08-23 15:52 UTC (7 hours ago)
(HTM) web link (www.science.org)
(TXT) w3m dump (www.science.org)
| kurupt213 wrote:
| Maybe we should stop perfluorinating every organic molecule
| perihelions wrote:
| Octa _nitro_ cubane also exists (first synthesized in 1999), and
| is the high explosive with the highest known detonation velocity.
| I think the bond strain in the cubane structure is a large factor
| in that.
|
| https://en.wikipedia.org/wiki/Octanitrocubane
| KSteffensen wrote:
| I think having as many nitro groups as carbons in there might
| also be a factor
| notimpotent wrote:
| I love how excited the author is about this post. It sounds like
| some promising discoveries are in the works.
|
| Of course I have no idea what any of this means. Maybe somebody
| could share a layman's explanation? What would be the benefit of
| "hold a free electron in the middle of that cube"?
| btilly wrote:
| The excitement is that someone did a lot of work and verified
| we got the science right on a bizarre compound.
|
| How to explain it? Let's go to the foundations. Let's start
| with the periodic table:
| https://en.wikipedia.org/wiki/Periodic_table.
|
| Matter is made up of atoms. Each atom has a nucleus and a cloud
| of electrons around it. Inside the nucleus we have some number
| of protons and neutrons. The number of protons determines which
| element it is. The number of protons + neutrons is basically
| how heavy it is - that's called an isotope. Isotopes don't
| matter for chemistry, so we'll ignore that.
|
| For example if you have 6 protons then you're the 6th element.
| Namely carbon. And 9 electrons gives the 9th element, fluorine.
| Also protons carry a positive charge, so you'd generally have
| the same number of electrons as protons. But not always. If an
| atom or molecule has a different number of electrons and
| proteins then it is called an ion. More on that soon.
|
| Next up, we have quantum mechanics. In a classical world, the
| electrons would want to go to the nucleus to hang out with the
| protons. In a quantum mechanical world, uncertainty in position
| times uncertainty in momentum has a minimum. Since electrons
| are light, if we know that an electron is in the nucleus, it
| probably has a momentum so big that it will soon NOT be in the
| nucleus. Therefore the best that the electron can do is be
| somewhere in a kind of probability cloud around the nucleus.
| Those clouds are called orbitals.
|
| The exact shapes of those clouds have been worked out, and are
| called orbitals. Orbitals form into shells. Each orbital can
| contain 0, 1 or 2 electrons. Each shell has a finite (usually
| fairly short) list of orbitals in it, and all of this has been
| worked out. This is why the periodic table (see
| https://en.wikipedia.org/wiki/Periodic_table again) is arranged
| into columns. Each column usually has the same stuff in its
| outer shell, and therefore is likely to do somewhat similar
| things chemically.
|
| Most of chemistry comes from one rule. Atoms like having their
| outer shell either totally empty, or totally full. They have 2
| ways to do. The first is the _ionic bond_. That 's where one
| atom gives another an electron, making both into ions. The ions
| then hang out together and are called a salt. The second is a
| _covalent bond_ , where 2 atoms share an electron each to give
| each an extra part time electron, making both happy. In the
| periodic table the farther towards the right and top you are,
| the more you want a full outer shell. And the farther towards
| the left and bottom you are, the more you are willing to give
| up electrons if someone asks.
|
| In fact the elements on the left side care so little for their
| outer electrons that, when they get together, they let their
| outer electrons wander around freely. Those electrons make
| things shiny, and conduct a current when they all move
| together. Those are metals. By contrast the ones on the right
| are non-metals - they can steal from metals or share with each
| other. How many depends on which column they are in.
|
| The very last column is the noble gases. They have a full outer
| shell and would like it to remain that way, thank you very
| much. So they don't get involved in this chemistry nonsense.
|
| Now let's talk about the stuff involved in this article.
|
| Fluorine, element 9, is the farthest to the top and right you
| can get without being a noble gas. It wants one electron and is
| vicious about getting it. Trying to get it do something unusual
| usually requires making it temporarily very unhappy. An
| unhappiness that it is perfectly willing to resolve by reacting
| with the chemist. This is not an idle threat - histories of
| fluorine usually start with a list of famous chemists who were
| killed or maimed in this way. However once it has reacted, it
| is often very stable. We stick fluoride into toothpaste and
| cook with teflon - both of which contain fluorine.
|
| Carbon, element 6, comes 3 columns before. Its outer shell has
| 3 fewer electrons, so it wants 3 more. Making 4 bonds. But
| where fluorine is vicious, carbon is polite. This makes carbon
| the tinker toy of complex chemistry. Which is how it became the
| backbone of pretty much everything required for life as we know
| it.
|
| Now what does this compound look like?
|
| Let's start with a box. At each corner you put a carbon. Each
| corner is connected by edges to 3 other corners. That leaves
| each carbon short one bond. So we stick one fluorine off of
| each corner. That gives us the diagram at the top right of the
| article.
|
| Now remember that fluorine is vicious, while carbon is polite.
| Yes, each fluorine is sharing an electron with a carbon, but it
| is rather unequal. The electron hangs out with the fluorine a
| lot more than with the carbon. Therefore the fluorines wind up
| negatively charged (the extra electron spends more time with
| them). The carbon atoms therefore wind up with a corresponding
| positive charge. And all of these positive charges, in theory,
| make the very center of the box a perfect place for a passing
| electron to take up residence. An electron that is not part of
| any atom, just sitting there enjoying a nice home. That extra
| free electron where an electron normally wouldn't be makes the
| whole thing an ion.
|
| So it is cool that the theory works out. But in order to do it,
| some chemist had to do stuff with fluorine that nobody sane
| wants to happen anywhere near them, let alone be actually doing
| doing in a lab.
| qorrect wrote:
| I like your word choices can you teach me chemistry ? /s
|
| No but really if you have any book suggestions for an
| engineer wanting to learn more chemistry I would appreciate
| it!
| bonzini wrote:
| So the anion is simply C8F8+ ? That is weird indeed.
| nanofortnight wrote:
| C8F8-
|
| The extra electron makes it negatively charged by -1 (thus
| an anion).
| sulam wrote:
| His excitement is due to the unlikeliness of the result, more
| than its usefulness. All of the compounds discussed are
| amazingly reactive, and working with them, even in a lab, is
| incredibly difficult.
| cosmojg wrote:
| The way this guy writes about organic chemistry has me swooning.
| beanders wrote:
| What are the potential applications? I read the article, it was
| pretty interesting but I only saw things that would be odd to an
| expert (which I am not). Sure it's a cool shape, but what does it
| do?
| samus wrote:
| It seems that it was evidence for theoretical approaches to
| predict molecule bond behavior. The author mentions DFT, which
| I assume stands for Density Functional Theory.
| chrisbrandow wrote:
| Yes
| doug_life wrote:
| Derek Lowe's "Things I Won't Work With" entire series is both
| educational and highly amusing. This is another good article:
| https://www.science.org/content/blog-post/sand-won-t-save-yo...
| narrator wrote:
| Hydrofluoric acid, mentioned in the article, is terribly toxic
| stuff. I can see why he doesn't want to work with it. A drop of
| the concentrated liquid on the skin can kill. Unfortunately, I
| think it's critical to the semiconductor industry and there's
| nothing that could conceivably replace it.
| tolstoshev wrote:
| This one is my favorite: https://www.science.org/content/blog-
| post/things-i-won-t-wor...
| greenbit wrote:
| "At seven hundred freaking degrees, fluorine starts to
| dissociate into monoatomic radicals, thereby losing its
| gentle and forgiving nature."
|
| Lol - that's the best
| ryandvm wrote:
| Yeah, reading this article I was amused with the author's
| writing style and reminded of the "Things I Won't Work With"
| blog. Lo and behold, it's the same guy.
| EricE wrote:
| Along the same lines he reminds me of one of my favorite
| youtubers: https://www.youtube.com/c/styropyro
| [deleted]
| UncleSlacky wrote:
| Similarly, "Ignition!" is a classic of the genre:
|
| http://www.sciencemadness.org/library/books/ignition.pdf
| selimthegrim wrote:
| Maybe I'm slow here, but the authors said they couldn't get a
| molecular ion in mass spec, but the ESR shows an electron in the
| center like would be expected for an anion? Is that a radical?
| Did they mean they couldn't get a cation?
| bilsbie wrote:
| Would this be useful for quantum computing somehow?
|
| Or maybe some kind of sensor?
|
| Also could a cell be programmed to make this or do cells not have
| the ability to manipulate flourine?
| metalliqaz wrote:
| If I'm reading the article right, the material is not stable
| (and also very very difficult to make). So I'm guessing this is
| probably just an interesting project to check how well current
| atomic bonding models fit reality.
| cscheid wrote:
| Lowe is being funny and calling back to his classic "Things I
| won't work with" series (which is also linked to in a
| different comment).
|
| One of the things you learn just from that series is that
| anything with this much fluorine jammed into it is just
| asking for trouble. Case in point,
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
| paulmd wrote:
| Azidoazole Azide is another classic from the "take a nasty
| little functional group and build a whole molecule out of
| them" family.
|
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
|
| Fulminates and Azides are known for their physical
| sensitivity, they're the primary explosive used for the
| primers in gun cartridges. Azides are generally more
| sensitive than fulminates - mercury fulminate is an older
| primer compound where mercury azides are quite unstable and
| reactive.
|
| Azidoazole Azide is basically an azide group bonded to an
| azole ring... azole is like pentane except with a nitrogen
| ring. So basically just one giant pile of nitrogen bonds
| looking for a reason to un-bond.
|
| See also, Hexanitrohexaazaisowurtzitane, although the name
| isn't nearly as suggestive, but that's a nice little
| molecular diagram right there too lol. "Thrillingly
| nitrogenated", would probably be the description.
|
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
| UncleSlacky wrote:
| See also "Ignition!":
| http://www.sciencemadness.org/library/books/ignition.pdf
| daniel-cussen wrote:
| Am reading it upon your recommendation!
| astrange wrote:
| I still want to know what isocyanide smells like. The "it
| smells bad" articles just say things smell bad but not
| exactly how.
|
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
|
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
|
| https://www.science.org/content/blog-post/things-i-won-t-
| wor...
| mkarliner wrote:
| It's always such a joy reading these posts. I'm not a chemist,
| although my father would have loved me to be, but the sheer style
| and erudition, makes them compulsive reading
| Alan_Dillman wrote:
| "Forget everything you know about slipcovers."
|
| I also had no expectations about something called
| Perfluorocubane.
| gtmitchell wrote:
| Wow, someone pulled off that synthesis? I'm impressed!
|
| For those who are wondering if this has any practical
| applications, the answer is almost certainly no. At best, someone
| might look at the synthetic pathways used to produce
| perfluorocubane to attempt to make something similar. It has
| really unusual spectroscopic and physical properties, which is
| pretty cool, but mostly in the sense of being a curiosity rather
| than being something you can do something with.
|
| Imagine this as being the chemistry version of someone managing
| to get Doom to run on an electric toothbrush or something. It's
| interesting and amusing to know it's possible, but you're never
| actually going to start using your Sonicare for gaming.
| dudeinjapan wrote:
| It's a Time Cube. In a single rotation of the octafluorocubane,
| each Time corner point rotates through the other 3-corner Time
| points, thus creating 16 corners, 96 hours and 4-simultaneous
| 24-hour Days within a single rotation.
| vitiral wrote:
| So it looks like a British phone booth and transports a
| Doctor around the Galaxy?
| jrumbut wrote:
| I always get Time Lords and Time Cubes confused.
| nextaccountic wrote:
| Could this thing be attached to a solid substrate, perhaps a
| semiconductor, and remain in place? Like in a computer chip
|
| What about using that free electron in the middle to do
| computing? Perhaps a quantum computer or something
|
| I mean that's what reminded me: quantum computers often trap a
| charged particle, perhaps an ion or electrons, and use it to
| store qubits. This stuff here seems to be a perfect electron
| trap. Or isn't it?
|
| (note, I'm just throwing ideas in the air, I know almost
| nothing of chemistry, semiconductors or quantum computers)
| YakBizzarro wrote:
| Not far from reality, indeed. Every time you have some
| molecule with a free electron, you can perform Electron Spin
| Resonance on it. You take a small amount of the molecule, put
| in a strong magnectic field, and with microwave you could
| drive the transition between the down and up state (parallel
| and antiparallel to the magnetic field). However, with a
| conventional spectrometer you can't control a single spin,
| because its signal would be tremendosly low, you would need
| at least ~10^13 molecules (maybe even less nowadays). If you
| want to use a single molecule, you need to connect to some
| kind of nanofabricated structure, in order to control and
| read it out. It's feasible, many works showed that, but very
| very difficult to engineer. You could spend most of your phd
| trying that (a pretty common tale in the field).
| throwawaymaths wrote:
| That's actually not a terrible idea! But sadly the ion seems
| to be unstable, which means ithe electron is not 'trapped'
| and rather free to interact with it's cage.
| Pulcinella wrote:
| Regular cubane and related compounds have been investigated as
| race fuels. The bond angles means that extra energy is stored
| (basically via tension in the bonds due to those extreme
| angles) compared to 4 ethane molecules (which add up to the
| same number of carbon atoms, hydrogen atoms, and bonds as one
| cubane molecule). So your race car could weigh less while still
| having just as much fuel energy. I think most race series have
| standardized fuel across competitors now so it's unlikely
| anyone will continue with the research.
| mcguire wrote:
| Dang it! And I was just getting together venture capital for
| industrial scale production.
| atwood22 wrote:
| Wouldn't having an ion like this be useful? I'm not an expert
| in Chemistry, but most ions will either return or gain an
| electron at the first opportunity. This compound, on the other
| hand, likes having an extra electron.
| daniel-cussen wrote:
| Yeah it opens up possibilities. Not worth patenting it or a
| near-neighbor.
|
| But this will lead places.
|
| In addition reduce search spaces. That's what it's all about
| with molecules these days. Search spaces.
| londons_explore wrote:
| This comments section doesn't look so different to one under a
| youtube video about how to make 'free energy' from water.
|
| When a lot of people pile in with their opinion on a topic they
| don't understand...
| blackoil wrote:
| At least, the tone suggests people are aware of the fact that
| they know nothing about the topic. On Youtube everybody is an
| expert on 'Free Energy'.
| jquery wrote:
| Can someone explain exactly how weird it is? It sounds like a
| monster was created but I don't really understand its properties
| beyond it being very acidic (?)
| devilbunny wrote:
| You have a sterically strained carbon structure (it does NOT
| want to make a cube). Then you saturate it with the one of the
| most aggressive atoms in existence, all without blowing up the
| carbon structure or your lab.
|
| That molecule would _really_ like to blow up.
| PlasmonOwl wrote:
| Just to weigh in as a chemist. A high level of skill and patience
| went into the creation of this. Fluorine is one of the nastiest
| things youll find in a lab. HF is no joke.
| sudosysgen wrote:
| There is a video series on YouTube of an organic chemistry PhD
| student attempting to synthesise cubane in his garage from
| readily accessible materials. It may put this feat into a bit of
| perspective as a non-chemist.
|
| https://youtube.com/playlist?list=PLnafk93vhO36cccP0p83hcop3...
| bediger4000 wrote:
| I like how the author assumed that readers have all kinds of
| abstruse chemical knowledge: lots of "as you would expect"
| phrases after chemical jargon.
| ufo wrote:
| This is an area where comment threads can shine. For most
| questions, if you ask it early enough then odds are that you'll
| get a good explanation from someone.
| anon_123g987 wrote:
| Every field does this trolling in some form. The sentence "The
| proof is trivial and left as an exercise to the reader." should
| be familiar for everyone who studied Math.
| mattkrause wrote:
| In that vein, this spoof captures the experience of reading a
| Springer "Introductory" textbook:
| https://kieranhealy.org/blog/archives/2022/05/20/every-
| sprin...
| gweinberg wrote:
| Hey, I'm reading a Springer book now, and it's not so bad.
| It's humbly titled "All of Statistics", and I think I
| understand at least 2/3 of it. So far.
| anon_123g987 wrote:
| Nah, it's standard engineering procedure:
| https://i.imgur.com/rKPe0Av.jpeg
| jordan_curve wrote:
| I never took anything past high school chemistry and I managed
| to understand it. It's not really that abstruse. My background
| is a bunch of wikipedia articles and chemistry youtube videos.
| devilbunny wrote:
| It's not a general-purpose blog.
|
| My B.S. in chemistry is 25 years old, and I still got the story
| despite not working in the field [edit:sp]since. It should make
| sense if you've had organic and qualitative analytical
| chemistry, which are sophomore- and junior-level undergrad
| classes. _Given his audience_ , that's pretty reasonable.
| dekhn wrote:
| I will never forget the diels alder reaction. 30 years since
| I took o-chem
| dvh wrote:
| I have a conjecture that if you visit some exotic materials'
| Wikipedia page and in top right corner is not something you can
| touch, it's probably a scam.
| yuan43 wrote:
| Synopsis:
|
| 1. Quantum mechanics predicts that the target molecule can
| accommodate an electron inside (electron-in-a-cube).
|
| 2. A sample of the target molecule was prepared, and yes, it
| involved elemental fluorine, a very difficult substance to handle
| safely and one notorious for nonproductively chewing up just
| about everything you give it.
|
| 3. Analytical results were consistent with the structure.
|
| 4. The substance's electrochemistry at low temperatures was
| consistent with the uptake of an electron at the predicted
| potential. Fine structure of results are consistent with the
| electron-in-a-cube idea. At room temperature, the results
| indicate decomposition.
|
| 5. Bonus: the electrochemical results suggest the electron-in-a-
| cube assembly is rotating unexpectedly.
|
| This is a really good example of basic science in action.
| Observation (some molecules envelop other molecules),
| generalization (maybe a molecule could envelop an electron),
| hypothesis (calculations suggest _this_ envelope in particular
| would work, and would yield these specific observations),
| experiment (figure out how to make the thing, make it, then
| measure the predicted properties), update hypothesis (in this
| case, the electron-in-a-cube is rotating unexpectedly).
|
| It's also a good example of why it's a good idea to do
| experiments you think will "work". Sometimes they don't work and
| your hypothesis does in fact suck. Sometimes they work exactly as
| you expect and you can add that to the pile of evidence you
| already have in support of the hypothesis. And sometimes you get
| a surprise.
| [deleted]
| perihelions wrote:
| Just checking, this experiment *confirms* that there's a lone
| electron inside the cubane cage?
|
| - _" At very low temperatures (77K, matrix isolation) in an ESR
| apparatus, though, you can indeed see the spectrum of the
| predicted "electron in a cube", split just the way that you would
| have drawn it out."_
|
| (It's written for an audience who doesn't need to be reminded
| that "ESR" means Electron Spin Resonance, and that is not me!)
| ajkjk wrote:
| > You will note the explanatory style that is characteristic of
| my long-delayed book, "Quantum Mechanics: A Hand-Waving
| Approach".
|
| I would read the crap out of this.
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