4 ms·

These are real compounds

196 points by _Microft 5y ago

_Microft 5y ago
I knew that cyclobutane existed (a ring of four carbon atoms with attached hydrogen atoms which is 'weird' in the sense that the angles between the bonds are not what would be expected for a carbon atom with four bonds [0]) but learned about the existence of ladderanes today. Their structure looks just soo unusual. https://en.wikipedia.org/wiki/Ladderane https://en.wikipedia.org/wiki/Ladderane Speaking of unusual structures, here is something like a 2D version of a ladderane: https://en.wikipedia.org/wiki/Fenestrane https://en.wikipedia.org/wiki/Fenestrane [0] https://en.wikipedia.org/wiki/Orbital_hybridisation#sp3 https://en.wikipedia.org/wiki/Orbital_hybridisation#sp3
- jihadjihad 5y ago
  It's interesting that one group of compounds is named using the Latin, in this case for "window" (fenestrane), but "ladderane" makes use of an ordinary English word (by way of Old English and Germanic). I guess I would have expected a Latin-derived name like "escalane" instead.
  - _Microft 5y ago
    Follow the first link/s in these articles and somewhere you will find „jawsamycin“. A part of this molecule looks a lot like a row of teeth…
    - Someone 5y ago
      Shark teeth (https://mobile.twitter.com/germhuntermd/status/1285971314134577152 https://mobile.twitter.com/germhuntermd/status/1285971314134...)
      - stavros 5y ago
        Oh and it contains luciferase?
  - ray__ 5y ago
    The common names for compounds/compound classes like this are usually just left to the person that discovers them. The standardized naming scheme is set by the IUPAC and the name that you get for any reasonably complicated molecule will be a mouthful.
    - gilleain 5y ago
      A mouthful? You're not wrong ... https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132927 https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132927 "8-[(1S,2R,3R,4S,6S,7S,8S,9S,12R)-pentacyclo[6.4.0.0^2,7.0^3,6.0^9,12]dodecan-4-yl]octanoic acid" Not sure how I would format the ring closure notation (like 0^2,7 is meant to be superscript)
- kccqzy 5y ago
  And the last example from the article, a tetrasubstituted cyclobutane, probably tells you that the functional groups connected to the cyclobutane could alleviate some of the ring strain in plain cyclobutane. Similarly, cyclopropane also has incredible ring strain and likely won't be found in nature, but plenty of derivatives can.
  - jamesash 5y ago
    Interestingly, cyclobutane and cyclopropane do not have a large difference in ring strain (within about 4% of each other). Cyclopropanes are well known in natural product structures. One of the weirdest is this natural product, U-106305, which has 6 cyclopropanes. Made by a strain of Streptomyces! https://pubs.acs.org/doi/pdf/10.1021/ja9619420 https://pubs.acs.org/doi/pdf/10.1021/ja9619420
- divbzero 5y ago
  I glanced at the structures first before reading the text and assumed they were oddballs synthesized in the lab. It’s incredible that these are all natural products. Leptocillin also looks astonishingly weird.
- derefr 5y ago
  > here is something like a 2D version of a ladderane Don't know about that analogy. To me, the 3D version of a fenestrane wouldn't be a ladderane, but rather an https://en.wikipedia.org/wiki/Adamantane https://en.wikipedia.org/wiki/Adamantane
rossdavidh 5y ago
"Pipline" -> "Pipeline"
- _Microft 5y ago
  Thanks, fixed!
- rossdavidh 5y ago
  An odd thing to downvote...
- deleted 5y ago
  [deleted]
moron4hire 5y ago
Always love a good Derek Lowe article. His article "Things I Won't Work With: Dioxygen Diflouride" is terrifying and hilarious at the same time. https://www.science.org/content/blog-post/things-i-won-t-work-dioxygen-difluoride https://www.science.org/content/blog-post/things-i-won-t-wor...
- mech422 5y ago
  I love that column :-) 'foof' is more then a cpu bug :-P
- thehappypm 5y ago
  His face is one I started noticing! He seems to have written tons of articles I really enjoyed
  - moron4hire 5y ago
    It's not my space, so I don't often read his articles or necessarily recognize his name when it comes up. For me it's the writing style and fear of flourine that I end up recognizing.
    - andybak 5y ago
      And his joy in finding new adjectives to describe bad outcomes.
- malux85 5y ago
  That was excellent, it just kept building!
echelon 5y ago
I'm ever conflicted with the opposing forces of climate change and meeting the energy needs of our growing and innovative civilization. Evolution has produced a bountiful assortment of living, breathing solutions that fit into every nook and cranny of our biological state space. Millions of years of adaptation have produced sometimes incredibly niche systems that beautifully capture all of the energy available to them. The biochemical pathways nature discovers are fascinating and complex and of an altogether different nature than what our human innovation capital can find or produce. So it's incredibly depressing that we're losing all of this amazing biodiversity. A moss or fungus might have more information in its genes - biochemical pathways, metabolic flux, finely tuned balance, encodings of adaptations beyond our understanding, etc. etc. - than the sum total of all human thought thus far. And that's not even considering the non-molecular, ecosystem and even biogeochemical impact these losses can have. But if we stop building and consuming and making, the plates come crashing down. Our sun burns out. The universe will never know of us. It's all so complicated. I'm glad we can appreciate these little wonders, though. Thank you for posting this article. Chemistry is beautiful.
- Maursault 5y ago
  > Chemistry is beautiful. It is, but as a species, we have been astoundingly irresponsible with it and continue to be, for profit.
- EdwardDiego 5y ago
  > The universe will never know of us. If there is anything out there with the capacity to "know", perhaps one day they'll find our ruins and compose some art along the lines of Shelley's poem Ozymandias. As I've been enjoyed the sci-fi of Adrian Tchaikovsky of late[0], I hope that it's sentient octupuses who can express the tragedy and mystery of our downfall in a dance of colour and movement. [0]: https://lareviewofbooks.org/article/we-are-going-on-an-adventure-on-adrian-tchaikovskys-children-of-ruin/ https://lareviewofbooks.org/article/we-are-going-on-an-adven...
zamalek 5y ago
"Extractions and Ire" on YouTube has been having a go at synthesizing a cubane, while the creator does "meme" a lot, it is good chemistry. And a really weird molecule.
- bpye 5y ago
  His main channel, Explosions and Fire, is also well worth checking out. Less focus on the chemistry and more of a focus on things that go bang.
- gilleain 5y ago
  There are a number of 'platonic hydrocarbons', like tetrahedrane, cubane, dodecahedrane https://en.wikipedia.org/wiki/Platonic_hydrocarbon https://en.wikipedia.org/wiki/Platonic_hydrocarbon Weird in a way, but not totally unexpected. Similarly Fe-S clusters form cubic shapes.
stevespang 5y ago

196 points by _Microft 5y ago

I knew that cyclobutane existed (a ring of four carbon atoms with attached hydrogen atoms which is 'weird' in the sense that the angles between the bonds are not what would be expected for a carbon atom with four bonds [0]) but learned about the existence of ladderanes today. Their structure looks just soo unusual. https://en.wikipedia.org/wiki/Ladderane https://en.wikipedia.org/wiki/Ladderane Speaking of unusual structures, here is something like a 2D version of a ladderane: https://en.wikipedia.org/wiki/Fenestrane https://en.wikipedia.org/wiki/Fenestrane [0] https://en.wikipedia.org/wiki/Orbital_hybridisation#sp3 https://en.wikipedia.org/wiki/Orbital_hybridisation#sp3

jihadjihad 5y ago
It's interesting that one group of compounds is named using the Latin, in this case for "window" (fenestrane), but "ladderane" makes use of an ordinary English word (by way of Old English and Germanic). I guess I would have expected a Latin-derived name like "escalane" instead.
- _Microft 5y ago
  Follow the first link/s in these articles and somewhere you will find „jawsamycin“. A part of this molecule looks a lot like a row of teeth…
  - Someone 5y ago
    Shark teeth (https://mobile.twitter.com/germhuntermd/status/1285971314134577152 https://mobile.twitter.com/germhuntermd/status/1285971314134...)
    - stavros 5y ago
      Oh and it contains luciferase?
- ray__ 5y ago
  The common names for compounds/compound classes like this are usually just left to the person that discovers them. The standardized naming scheme is set by the IUPAC and the name that you get for any reasonably complicated molecule will be a mouthful.
  - gilleain 5y ago
    A mouthful? You're not wrong ... https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132927 https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132927 "8-[(1S,2R,3R,4S,6S,7S,8S,9S,12R)-pentacyclo[6.4.0.0^2,7.0^3,6.0^9,12]dodecan-4-yl]octanoic acid" Not sure how I would format the ring closure notation (like 0^2,7 is meant to be superscript)
kccqzy 5y ago
And the last example from the article, a tetrasubstituted cyclobutane, probably tells you that the functional groups connected to the cyclobutane could alleviate some of the ring strain in plain cyclobutane. Similarly, cyclopropane also has incredible ring strain and likely won't be found in nature, but plenty of derivatives can.
- jamesash 5y ago
  Interestingly, cyclobutane and cyclopropane do not have a large difference in ring strain (within about 4% of each other). Cyclopropanes are well known in natural product structures. One of the weirdest is this natural product, U-106305, which has 6 cyclopropanes. Made by a strain of Streptomyces! https://pubs.acs.org/doi/pdf/10.1021/ja9619420 https://pubs.acs.org/doi/pdf/10.1021/ja9619420
divbzero 5y ago
I glanced at the structures first before reading the text and assumed they were oddballs synthesized in the lab. It’s incredible that these are all natural products. Leptocillin also looks astonishingly weird.
derefr 5y ago
> here is something like a 2D version of a ladderane Don't know about that analogy. To me, the 3D version of a fenestrane wouldn't be a ladderane, but rather an https://en.wikipedia.org/wiki/Adamantane https://en.wikipedia.org/wiki/Adamantane

rossdavidh 5y ago

"Pipline" -> "Pipeline"

_Microft 5y ago
Thanks, fixed!
rossdavidh 5y ago
An odd thing to downvote...
deleted 5y ago
[deleted]

moron4hire 5y ago

Always love a good Derek Lowe article. His article "Things I Won't Work With: Dioxygen Diflouride" is terrifying and hilarious at the same time. https://www.science.org/content/blog-post/things-i-won-t-work-dioxygen-difluoride https://www.science.org/content/blog-post/things-i-won-t-wor...

mech422 5y ago
I love that column :-) 'foof' is more then a cpu bug :-P
thehappypm 5y ago
His face is one I started noticing! He seems to have written tons of articles I really enjoyed
- moron4hire 5y ago
  It's not my space, so I don't often read his articles or necessarily recognize his name when it comes up. For me it's the writing style and fear of flourine that I end up recognizing.
  - andybak 5y ago
    And his joy in finding new adjectives to describe bad outcomes.
malux85 5y ago
That was excellent, it just kept building!

echelon 5y ago

I'm ever conflicted with the opposing forces of climate change and meeting the energy needs of our growing and innovative civilization. Evolution has produced a bountiful assortment of living, breathing solutions that fit into every nook and cranny of our biological state space. Millions of years of adaptation have produced sometimes incredibly niche systems that beautifully capture all of the energy available to them. The biochemical pathways nature discovers are fascinating and complex and of an altogether different nature than what our human innovation capital can find or produce. So it's incredibly depressing that we're losing all of this amazing biodiversity. A moss or fungus might have more information in its genes - biochemical pathways, metabolic flux, finely tuned balance, encodings of adaptations beyond our understanding, etc. etc. - than the sum total of all human thought thus far. And that's not even considering the non-molecular, ecosystem and even biogeochemical impact these losses can have. But if we stop building and consuming and making, the plates come crashing down. Our sun burns out. The universe will never know of us. It's all so complicated. I'm glad we can appreciate these little wonders, though. Thank you for posting this article. Chemistry is beautiful.

Maursault 5y ago
> Chemistry is beautiful. It is, but as a species, we have been astoundingly irresponsible with it and continue to be, for profit.
EdwardDiego 5y ago
> The universe will never know of us. If there is anything out there with the capacity to "know", perhaps one day they'll find our ruins and compose some art along the lines of Shelley's poem Ozymandias. As I've been enjoyed the sci-fi of Adrian Tchaikovsky of late[0], I hope that it's sentient octupuses who can express the tragedy and mystery of our downfall in a dance of colour and movement. [0]: https://lareviewofbooks.org/article/we-are-going-on-an-adventure-on-adrian-tchaikovskys-children-of-ruin/ https://lareviewofbooks.org/article/we-are-going-on-an-adven...

zamalek 5y ago

"Extractions and Ire" on YouTube has been having a go at synthesizing a cubane, while the creator does "meme" a lot, it is good chemistry. And a really weird molecule.

bpye 5y ago
His main channel, Explosions and Fire, is also well worth checking out. Less focus on the chemistry and more of a focus on things that go bang.
gilleain 5y ago
There are a number of 'platonic hydrocarbons', like tetrahedrane, cubane, dodecahedrane https://en.wikipedia.org/wiki/Platonic_hydrocarbon https://en.wikipedia.org/wiki/Platonic_hydrocarbon Weird in a way, but not totally unexpected. Similarly Fe-S clusters form cubic shapes.

stevespang 5y ago