Cubane Lore
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- Опубликовано: 30 июл 2024
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Cubanes are a pretty neat class of molecules - in this video, we explore the applications of cubanes, and rank some impressive cubanes such as BUTTERCUBE!
Summary
In this, the host discusses Cubane, a cube-shaped molecule, and its potential applications in medicinal chemistry. Cubane is considered as a substitute for Benzene rings in new drug candidates. The 3D structure of Cubane allows for distinct interactions with target proteins or receptors. Additionally, Cubane can have different metabolites compared to Benzene. It is also explored in energetic materials. The video presents a tier list of various Cubane derivatives, highlighting their structures and uniqueness.
Highlights
💡 Cubane is a cube-shaped molecule that medicinal chemists want to use as a substitute for Benzene rings in new drug candidates.
💡 Substituting a Benzene ring with Cubane in an active pharmaceutical ingredient (API) could potentially improve binding to the target.
💡 Cubane's 3D structure allows for different interactions in space, unlike the flat Benzene ring.
💡 Cubane derivatives can have different metabolites compared to Benzene, which is important for drug elimination from the body.
💡 Cubane is also explored in energetic materials, although its large-scale production poses challenges.
💡 The tier list of Cubane derivatives ranks them based on their impressive structures, with S tier being the most impressive.
💡 The video acknowledges the need for more commercially available and affordable Cubane derivatives to advance research and drug development.
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Team
Writer/Producer - That Chemist (Joey)
Editor/Lead Animator - ReformLabs
3D Systems Engineer - Robot Chicken
Thumbnail Artist - RinFroggy
Acknowledgements
Thanks to the people on Twitter who helped suggest cubane references! Especially Kitspiroplatin for the reference of the extremely long tetracubane iodide! I also want to acknowledge that Tom will eventually make cubane.
References
Tom’s Cubane Series • Cubane Synthesis
Perfluorocubane • The First Real Life Pi...
Chemiolis Click Chem • Click Chemistry in Act...
Casual Chemistry Click Chem • Copper and Click Chemi...
Cubane Review Articles:
Cubanes in Med Chem doi.org/10.1021/acs.jmedchem.8...
Cubanes: 50 Years Later doi.org/10.1021/cr500523x
Bicubyl pubs.acs.org/doi/10.1021/ja98...
bidentate cubane ligand doi.org/10.1055/s-0029-1217083
butter cubane doi.org/10.1016/S0040-4039(00...
carboxycubane thioxanthylglycine - worldwide.espacenet.com/paten... (page 48)
cubane carboxylic acid doi.org/10.1002/chem.201901086
cubane dicarboxylic acid dimethyl ester doi.org/10.1055/s-0040-1705964
cubane doi.org/10.1055/s-1995-3961
cubene doi.org/10.1021/ja00229a057
cubyl phenyl ketone pubs.rsc.org/en/content/artic...
cubyl triflate pubs.acs.org/doi/abs/10.1021/...
cubylmethanol doi.org/10.1021/ol501750k
dideuterocubane pubs.acs.org/doi/10.1021/jp95...
diethynyl cubane pubs.acs.org/doi/abs/10.1021/...
diflucuburon doi.org/10.1002/anie.201510675
letepricube worldwide.espacenet.com/paten...
mercury cubane insanity doi.org/10.1021/cr500523x (compound 71)
methoxycarbonylcubane carboxylic acid - 10.1002/chem.201901086
octamethylcubane doi.org/10.1016/S0040-4039(00...
octacyclopropylcubane onlinelibrary.wiley.com/doi/a...
octanitrocubane doi.org/10.1002/(SICI)1521-37... (this DOI sucks)
octaphenylcubane pubs.acs.org/doi/abs/10.1021/...
perfluorocubane doi.org/10.1126/science.abq0516
perfluorooctamethylcubane pubs.acs.org/doi/abs/10.1021/...
tetracarbomethoxycubane link.springer.com/article/10....
tetrabromotetranitrocubane pubs.acs.org/doi/10.1021/jo97...
pedestal - doi.org/10.1002/anie.199214211
Molecules in this Tierlist
Bicubyl, bidentate cubane ligand, butter cubane, carboxycubane thioxanthylglycine, cubane carboxylic acid, cubane dicarboxylic acid dimethyl ester, cubane, cubene, cubyl phenyl ketone, cubyl triflate, cubylmethanol, dideuterocubane, diethynyl cubane, diflucuburon, letepricube, mercury cubane insanity, methoxycarbonylcubane carboxylic acid, octamethylcubane, octacyclopropylcubane, octanitrocubane, octaphenylcubane, perfluorocubane, perfluorooctamethylcubane, tetrabromotetranitrocubane, tetracarbomethoxycubane, tin cubane insanity, extremely long cubane, lead cubane insanity
Thanks to Factor75 for sponsoring today's video. Go to strms.net/ThatChemistFactorAprYT50 and use code POGCHEMISTAPR50 for 50% off your first box!
MOF
According to Pokémon Yellow, Cubane wears the skull of its dead mother as a helmet, and is known as the "Lonely Pokémon" because of its tendency to keep to itself and avoid social situations, due to the trauma caused by the death of its mother. On the night of a full moon, the cries are said to be especially terrible.
hey man i wanna access this insanity but i cant for some reason, it says i need register or something
Thank you.
Cubane whit copper what would it be called ? CuCubane
Tom, I know you are reading this, GO BACK TO YOUR THESIS! please :)
goddamn it
@@ExplosionsAndFire got you buddy
Ahh yez, yellow-chemisty-loving-Tom replied
@@ExplosionsAndFire lmao gotteem
@@ExplosionsAndFirelol
There’s a new theoretical carbon allotrope called “cubane diamond” made of stacked cubes. Take cubane units, make a checkerboard pattern with them, copy that pattern but offset it by one cube, stack it on top of the previous layer, and so on.
That carbon allotrope is stable under high pressure but cant be quenched to ambient conditions.
@@penteractgaming god if only
Lmao, you rascal :P
I need to find papers on this :)
Any chemist/material scientists want to explain what this material's physical characteristics would be like, in theory?
My first encounter with cubane was about 1966 at the University of Texas, on my Ph.D. qualifying exam. It was a "predict the product" question and I kept coming up with cubane... and I kept saying "that can't be right, that product would be unstable... it must rearrange." I ended up getting partial credit.
sneaky
I first heard of cubane by googling "Cubanate" (GT1 soundtrack).
I’m studying at UT for biochemistry! I’m in my first year right now!!
@@hi-im-morgan Hook 'em!
@@Fredpotts Hook ‘em!
Fun Fact: Tom's work with cubanes goes so far back that his fist video was actually recorded on a VHS that was later digitized and uploaded to RUclips.
We had a rocket design team at my university, and when thinking of fuel ideas someone jokingly said “Minecraft fuel would be funny” and that led to my cubane rabbithole
My Ochem professor is part of the group that won the Nobel Prize for click chemistry. Never have I seen a grown man be so excited for what he essentially described as "very small Lego"
It's good to see all the chemical RUclips channels showing love to each other.
:)
Is that what passes for love? To me it seemed more like an academic laying the heat on "yeah, but you haven't published yet".
@@EmyrDerfel hmmm, where do I start...
I realize this is a joke and ripping into someone because they haven't published their thesis yet IS pretty mean. Ja boy has it. Academica gate keeping is total bullshit, I agree! So is passive aggressiveness. Don't get me wrong, I'm a troll at heart too! My whole RUclips comment history is me having fun. I love skipping stones!!! I F*** with "smart people", it's not easy being smart. Oh yeah, love! It comes in many forms. It's the most powerful thing on our planet and very much can be used for good and evil 😉. You can talk shit out of love though.
You can't go wrong Voltron style. Together we can achieve much greater things!!!
they share a bond
@@smiggyballs4100 Good one! 😂
It’s so weird listening to this as an C.S. Major and hearing “APIs” in chemistry.
True, I didn’t even think about it
As a chemist student who dropped it for Computer science, maybe it can be used as an API for the human body 🤔
First found out about cubane in Hamilton Morris' podcast w/ Explosions and Fire. Then watched all of what he currently has in his garage cubane series. Good stuff
Thanks for sharing :D
Yea I haven't watched this video yet but I'm hoping that there would be a spot for octanitrocubane :D
8 minutes in and we have an S-tier :D
So the collab did happen.
My A-Level chemistry teacher told us in her PhD she did research making cubanes. It became an interest of mine after that, translation: my autism did an autism and I didn't want to leave the topic for a week straight.
I relate. Something tickles your brain and you inhale a savant level of information about it in weeks
@@ianharrison5758 definitely!
There's the hypothetical molecule Octaazacubane(N8), which would be 8 Nitrogens arranged in a cube like Cubane. It could also have the nickname "Nate".... ;)
I'd call it goodnight, because that's what you could say to the first person to synthesize it on any appreciable scale.
@@zockertwins Another hypothetical nitrogen compound that would be _super_ unstable = N(N3)3 or Triazinamine or Nitrogen Triazide.
Can't we just call it cubazide
@@kingflynxi9420 not bad!
How about octaazidocubane? It is not a nitrogen allotrope but it's C8N24!
Your editor is on adderall or something, I love it. The editing is nuts in this episode.
I went and did a final ADHD edit at the end of it ;)
I had seen the first E&F video about cubane but steered away because it looked like a scary long synthesis. Then, my organic chemistry professor saw that my friends and I were sketching out what we thought would be unreasonable species and shotgun told us about a bunch of weird organic molecules, including cubane since I had drawn a cube that my friend had labeled "bullshit." I have been obsessed since and blitzed through all of the E&F videos immediately after.
If you hold down the X button on the first controller, the GameCube makes different sounds when you start it (kind of bouncy, rubbery sounds). If you hold down the X button on all four controllers, you get a third set of sounds.
What’ll happen first, Tom getting his thesis finished or Tom making Cubane?
Plot twist: Tom is writing a cubane thesis
Well turns out it was the thesis
I think the first time I heard about it was back in college second level chemistry when we were learning about chemical bond strain and the professor kind of offhandedly brought ot up as an extreme example
Funny enough, Tom just put up a new update on Extrations&Ire. That's also the first time seeing cubane, watching some Explosions&Fire videos some years ago, got lab for my bachelor thesis in chemistry next month
Labrador retrievers indeed help with chemistry exams.
Still waiting for cubyne :(
I didn't know cubane lore was that deep
Now I (in the fourth year of my medicinal chemistry PhD) suddenly want to try to design a cubane-containing peptide drug candidate!
Let me know how it goes :)
What about the Single-layer materials tierlist ? Everyone has heard of graphene, but there are others that are a bit in its shadow. It will also be quick for you to draw them 😉
For me it was my beloved organic chemistry book (Vollhardt) which featured a couple of cubane molecules but the one that caught my eye was Octanitrocubane, right next to RDX. That book really was nuts. The older yours is, the more in-depth it goes about illicit drug manufacturing, synthesis of HE you name it ..
One one hand I would love to get samples of those cubanes for my collection, on the other hand I know that the volatile ones will just evaporate off unless I manage to seal them in an ampoule *without* setting them alight
Nice Video. And yes, we would watch a Video where each molecule goes into the category with its first letter. Because, we don't watch your videos because there are categorizations. We watch to learn about new molecules and love your personal touch.
At least me.
I gotta say I agree with you on the cubyl phenyl ketone. It looks so innocent and nice, and gives me inner peace.
That is a smooooth intro 👌 loving this vid so far
thank you :)
I'm fairly certain that when the cube structure fails in (...)fluorocubane, all those flying fluorine groups will do SOMETHING interesting xD
I’d love to see some cube psychedelics, they already have such complex structures to tickle certain 5HT2A receptors, adding a cube could make some really interesting substitutions if there’s somewhere good to chuck one in on say LSD. Awesome video!
Bro... What do you dislike about classical psychedelic structures? among them are full of simple effective biodegradable molecules. Have you played too much minecraft?
@@user-xr6rh5ke3v lmao just because we have stuff that works doesn’t mean there isn’t stuff out there that could work better
@@user-xr6rh5ke3vCuz maybe it would fuck you up different
Toms cubane synth was the first time hearing from it
Watching these ranking video again after a while and it seems he's slowly descending into madness with the tier lists.
😅
I first learned that cubanes exist in my high school organic chemistry class.
Our teacher was giving examples on intramolecular Wurtz reactions, in which a bond in cubane was replaced by vicinal chlorides
I learned about Cubane in Orgo class as an undergraduate, and when I was working on my senior project as a chem major (crystallography of solid keto-carboxylic acids), I desperately wanted to make acetylcubanecarboxylic acid, but I couldn’t figure out how to do it and my supervisor had no interest in chasing after challenging stuff like that.
I still want to make it, but 30 years of being a physical inorganic chemist (I went from crystallography to solid state NMR to inorganic pigment chemistry to teaching) later, I’ve forgotten what little I knew about organic synthesis and I don’t have access to an equipped synthesis lab anyway.☹️
I like how you called out Tom from explosions and fire lmao
Everyone needs to harass Tom. You know, so he can finish his thes...uuhhh to finish cubane!
Cubane got that angle strain out the asssssss
more like out the s, cause a cubane system has a bit of p character to it😎
You are one of my favourite channels, because of how quickly you talk. Usually I have to up the speed to 1.5x whenever I watch someone else, but you speak at a good speed
I love how you just don't care about the utility of the tierlist. Especially here it's just used as an excuse to talk about cool molecules while maintaining viewership. Great format :3 !
Cubanes were things made as soon as you get hold of a molecular modelling kit. I was thrilled to bits when returning to chemistry to find out that they were a thing. The first kit I had (long before Molymod) used springs as bonds and the strain made the model itself slightly dangerous - it really was energetic.
woah i JUST binged e&f's series. no joke i was watching ep 11 right when i saw this in my recommended.
my cubane origin story is that one of my organics lecturers offhandedly mentioned it in the first sem of this year (1st year undergrad) and i HAD to look it up right after
I have no actual knowledge about chemistry besides high school (which I failed because I can’t do math and the Mol section killed me) but the fact that molecules are “2D” and “3D” is blowing my mind.
they are technically always 3D, but they can be pretty flat
To me Cubane looks like it would be good for making inorganic Metal complexes based on it, considering Weird shaped cyclic compounds are used for that purpose alot,
true, but a cubane would be a VERY expensive ligand
not as bad as those BINAP ones tho lol
Love how around 13:35 the text you cited to the heavy water board has nothing to do with heavy water Lol
What intrigues me the most about Dideuterocubane is how much control you have about which two corners the D attaches to.
Ooooh the new research chem scene will be wild
I learned about Cubanes from the channel Explosions&Fire
awesome :)
(Non-chemists) Didn't we all? *sheds a tear*
I first learned about cubane when I was looking into hight energy explosives, such as ONC.
seems like you’re gonna need a new tier list template going forward, with S+ and beyond
I love that Tom from explosions and fire made a cubane video the day after this one saying he's restarting the project
I was thinking "I need a video to watch" and this is a video.
I learned about cubane when I thought if all organic molecules were flat and looked it up. My organic chemistry material is really subpar.
I also learned about conformations of cyclic compounds in that same way.
I have a lecture about Supramolecular Chemistry and Molecular Machines this semester and we talk a lot about click-chemistry since it's used there a lot.
RIP in peace Kurt Cubane
Explosions and Fire's series introduced me to the molecule
awesome :)
Tierlist suggestions: transition metal complexes, I've seen some weird ones out there. Or something to do with unintuitive bonding in compounds, boron hydrogens stuff looks weird at first in just Google images searches.
It was, naturally, the energetic materials thing that intoduced me to these.
Reading the bioisostere paper makes me wonder what if we make cubane-based fragrance compounds? Does 2-cubylethanol smell like roses and cubylmethyl acetate smell like jasmine? 4-Hydroxy-3-methoxycubanaldehyde vanilla and 4-(4-hydroxycubyl)butan-2-one raspberry? How about making a cubane analog of galaxolide?
I learned about cubane from that aussie Explosions and Fire guy. (Tom, he is.)
That man gave me a love for chemistry I didn't think I could have, planning on doing some independent study into chemistry.
Unfortunately, we may have to forget benzene if cubane takes it's place. But don't worry, it'll be back.
carboranes would be interesting to make drugs from as well. not only are there cubes and various other shapes, theyre very stable
I heard some of them are explosive tho
@@That_Chemist theres a huge gap in reactivity between boranes like B2H6 or B5H14 in the gas phase and C2B10R12 in solution. The former can ignite on contact with air and Boron-10 rich derivatives of the latter are being tested as targets of neutron radiation therapies for treating cancers. There was some concern about toxicity back in the 90s but the mechanism of this toxicity is unclear.
Im an environmental science major and certainly not into chemistry this heavily but i love watching your videos because i can hear you smiling. Youre so enthusiastic and its heartwarming
I learnt about it when I was 15 because I started organic chemistry and I was looking for interesting molecules(aromatic,cyclic etc) and came across it
That intro was fantastic. So nostalgic
people are LOVING Cubane! Absolutely bonkers for it!
I don't actually recall how I first came across cubane. It must have been around 2011. I think I was looking up the toxicity mechanism of strychnine, came from there to glycine antagonists, then to chinese very strong rat poison, and then molecules with comparable structures.
EDIT:
No, I started with high-viscosity fractions of petroleum, went from there to adamantane and asphaltenes and then cubane.
Great video, but I think it's important to note at 14:23 that Sharpless received a third of the nobel prize with Carolyn Bertozzi and Morten Meldal.
I might be stupid enough to accidentally have a cool idea. What about cubane with cubanes hanging off every corner, and their free corners and so on. Kind of a big fluffy crystal bush with branches you have to rake off the bench constantly. (Okay, imaging it vibrating from heat just happens to look cool and trippy in my head even if it can't exist in the real world for reasons I don't know about.)
love the new logo
Professor poliakoff and buttercubane that had me 💀
Swag vid. Med Chem video sounds cool (I am med Chem PhD student but moreso NeuroTox lol).
awesome - we have a whole bunch of medchem ppl in the TC Discord - you should check it out ;)
Are disubstiuted cubanes chiral? If yes which ones? I am nof sure if wr are seeing racemats here or if they just cannot be chiral.
They could be chiral if 2 adjacent substituents on corners of the cubane were different, while the 1,4 are both also substituted - I.e. it’s possible
Oh god yesss please someone make butter cube. I must live long enough to read this paper!
the intro was fire ngl ! hahahah
I need to see someone make the butter cube pretty please
NO WAY that photo is from the wing C downstairs lab, I think you TA'd one day of my orgo lab once AND the tutorials 🤯
I was casually looking at different stuff on MolView after a class and stumbled on Cubane, and thought "huh, that looks cool"
That time when I tried to make octanitrocubane in my shed almost yeeted myself with unstable flammable ~ instable reaction... Good time's 😂
Super! Thank you very much!
Is it possible to put multiple cubes together, or even have a cubic carbon crystal?
The "lead cubane insanity" looks like a cubane spider lol
Cubane Spider boss fight😂
i need to see that butter cube
does the double bond in cubene disociate like the ones in benzene or is it lacking the pi bonding necessary?
not to the extent that benzene does, but I have to assume that a portion of the electron density for those orbitals partially hybridizes with the cube
Listening to this video
This new format - hereafter "the format" - is good
Thank you :)
It's interesting how the cuban can change benzene in some API about spatial considerations . I think this kind of changes requires more research in the future, since I've heard only plain groups in the current theory.
Dunno where your focus is but propellanes as arene bioisosteres have been ubiquitous in the literature for at least the past decade.
You might want to check the slide at 13:36 . The graphical representation of 1.5mL of deuterated water per 1L of natural water is all wrong. it splits the 1L of water up in 10x10x10=1000 tiny cubes. 1L = 1000mL, so each cube should be 1mL, not 10mL as stated later. Therefore, there should be one and a half tiny cube of deuterated water in that 1L cube.
I've learned about cubane from your tierlist xD
I first learned about Cubane from Tom's hilarious videos.
I think I had heard about them once in class before that, but Tom was the first one to talk about them outside of my ochem class
Hopefully our friend Tom is able to make some octanitrocubane someday. Glad he was finally able to make cubane though!
I learned of cubanes from Tom, still following that project
I'm excited for cubane designer drugs.
Something about bicubyl tickles the same part of my brain that dewar benzene does.
Very cool
"Should be alright" Story of Explosions and Fires life.
I wonder when diflucuburon will go into regular production? It's a very promising insecticide, particularly against the rust red flour beetle where diflubenzuron isn't nearly as effective.
Octanitrocubane seems like it would be very oxygen rich, could replacing some of the nitro groups with methyl groups balance it out a bit?
I discovered it on a RUclips video from Science Trash (French RUclipsr) talking about dangerous chemicals, and in this video there was octanitrocubane.
I was like how a molecule can be cubic👀
I'd also add tricubylphosphine (analogue of triphenylphosphine) and related ligands (dcbpf = 1,1'-bis(dicubylphosphino)ferrocene, dcbpm = bis(dicubylphosphino)methane, dcbpe = 1,2-bis(dicubylphosphino)ethane), salen with cubane replacing benzene, and whatever ligand idea that I have.
i wonder if anyone has made tetrahedrane before. seems like it would make cubane look easy
*TC mentions perfluorocubane photos in other video*
"LOOK, GARY, THERE I AM!!"
What about octacubyl cubane? Like ictaphenyl cubane but with a cubane on each corner of the cubane?
Aight that intro was sick
It would be nice to see octaazacubane lol