5 ms·

The thing with randomly generating molecules is unlike with faces or cats, there is the good chance that a real molecule is generated. Unless they screen the mo

The thing with randomly generating molecules is unlike with faces or cats, there is the good chance that a real molecule is generated. Unless they screen the molecule against a database and exclude matches?

happytoexplain 5y ago
Are we sure that's the case? I have no idea what the combinatorics are like for molecules of this size. They seem small enough that it would occasionally generate molecules that have existed at some point, but that's based on some really fuzzy intuition.
- CrazyStat 5y ago
  I tried a few times, and on the second load of the page I got a single hydrogen atom, so I think it's safe to say they aren't excluding things. There was recently a link, I think on the front page here, to an article about how many chemical compounds there are [1]. Based on that link we're looking at probably trillions to quadrillions of potential structures with atomic weight under 300, which would cover the structures I saw in my few reloads of the page. Chemistry is wild. For an example close to home, taking table sugar (sucrose, a single type of molecule) and applying heat to caramelize it results in hundreds to thousands of different end products from at least half a dozen qualitatively different classes of chemical reactions. [1] https://www.chemistryworld.com/opinion/chemical-space-is-big-really-big/7899.article https://www.chemistryworld.com/opinion/chemical-space-is-big...
  - permo-w 5y ago
    the Maillard Reaction?
    - CrazyStat 5y ago
      The Maillard reaction is protein browning,separate from sugar caramelization
      - dekhn 5y ago
        both are very interesting both from a chemistry standpoint as well as a tasty standpoint.
  - csense 5y ago
    I never got far enough in chemistry to really figure out if it has explanatory or predictive power. If you ask a CS grad "What will happen if you run this program?" they should be able to predict it. If they've gone through nand2tetris they can explain it all the way -- compiler, OS, machine language, ALU / registers / bus, logic gates. If you ask a chemistry grad "What happens when you apply heat to this molecule?" can they predict it? Can you explain it all the way -- from molecules to atoms to electrons to quantum fields? If we can't predict "Okay this is what will happen if I mix these two substances together," how do we have a good scientific theory? I guess chemistry says we always end up with the same atoms we started with (unless you start to go nuclear by using energetic particles to modify the nucleus), but can we predict which of the zillions of possible rearrangements will actually happen? We know by experiment that H2SO4 is an acid, and that H2SO4 is a "legal" molecule in a way that HSO3 or H5S7O9 are not. Is there a way to figure this out from first principles? Can you figure out by inspecting the chemical formula that H2SO4 will be an acid if you didn't already know that ahead of time? Can you figure out that H2SO4 will be a "legal" molecule but H5S7O9 will not? Can you look at a reaction and tell whether it will "compile" and what it does, the same way you can look at a program and figure out if it will compile and what it does? If you can't, why not? And what use is a theory of chemistry that can't make concrete predictions? If you just have a list of known substances and reactions, is that even a theory, or is it just experimental data?
    - opportune 5y ago
      Computational chemistry answers some of these questions. When you look at just a molecule by itself “what happens if you apply heat” is somewhat simple. Covalent bonds just break because the molecule is vibrating too much - think of a covalent bond as a flexible strut, if you put too much pressure on it, it snaps. This can result in the temporary formation of unstable molecules that then recombine. You could predict which particular bonds in a molecule are unstable based on the total structure, angles, electronegativity, polarity, etc. But of course those small unstable molecules can further breakdown, react with each other, and react with the parent molecule to form new stuff. So basically the parent molecule is part of some huge “power set” of potential molecules all interacting with each other.
    - 5y ago
- aassddffasdf 5y ago
  Exactly.
arcticfox 5y ago
Yeah, unlike https://thispersondoesnotexist.com/ https://thispersondoesnotexist.com/, this could really use a small About section or ? to hover over. Either they do something clever to exclude real molecules, my understanding of chemistry is too limited (100% possible), or it's more like "this molecule might not exist"...
- dexwiz 5y ago
  More likely it’s not stable or no way to synthesize it. Complex molecules have internal “stress” that needs to be weaker than the individual bonds. Making explosives is often maximizing that stress while still making a viable molecule, kind of like a mouse trap.
  - semi-extrinsic 5y ago
    Nah. These are all predominantly branched and/or cyclic carbon chains, with a few heteroatoms scattered in for effect. They probably burn well, they might smell nasty, but they are not going to be explosive. Explosives (or "energetic materials" as they are known in the trade) are generally all about stuffing as many nitrogen and oxygen atoms as possible into your molecule; take TriNitroToluene as an example, it has 7 carbons, 3 nitrogens and 6 oxygens, and that's fairly mild. What these structures remind me most of is what you would find in a sour heavy crude oil. In fact, I can guarantee the person who named this website has never looked at high resolution mass spectroscopy analysis (like an FTICR-MS) of any type of petroleum, or they would have named it "this chemical is probably being pumped out of the ground right now".
    - dexwiz 5y ago
      Yes, practically this means shoving as many nitro groups together. But what makes nitro groups explosive to begin with? From what I remember, the large electron shells of the oxygen atoms repel each other, increasing the bond N-O-N angle by a few degrees. It's very easy to break these stressed bonds, and oxidize another carbon compound with the liberated oxygen, creating CO2 gas (the explosive bit). Some of the most powerful explosives are made by attaching nitro groups to stressed ring or cage structures.
t3po7re5 5y ago
For a quick check they could run the generated compounds through these databases Zinc15 - https://zinc15.docking.org/ https://zinc15.docking.org/ Chembl - https://www.ebi.ac.uk/chembl/ https://www.ebi.ac.uk/chembl/ Also as an aside I believe there's a current trend to generate chemical compounds by creating SMILES strings using BERT which is a cool way to incorporate language and chemistry (An example of a team doing that https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6 https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6)

happytoexplain 5y ago

Are we sure that's the case? I have no idea what the combinatorics are like for molecules of this size. They seem small enough that it would occasionally generate molecules that have existed at some point, but that's based on some really fuzzy intuition.

CrazyStat 5y ago
I tried a few times, and on the second load of the page I got a single hydrogen atom, so I think it's safe to say they aren't excluding things. There was recently a link, I think on the front page here, to an article about how many chemical compounds there are [1]. Based on that link we're looking at probably trillions to quadrillions of potential structures with atomic weight under 300, which would cover the structures I saw in my few reloads of the page. Chemistry is wild. For an example close to home, taking table sugar (sucrose, a single type of molecule) and applying heat to caramelize it results in hundreds to thousands of different end products from at least half a dozen qualitatively different classes of chemical reactions. [1] https://www.chemistryworld.com/opinion/chemical-space-is-big-really-big/7899.article https://www.chemistryworld.com/opinion/chemical-space-is-big...
- permo-w 5y ago
  the Maillard Reaction?
  - CrazyStat 5y ago
    The Maillard reaction is protein browning,separate from sugar caramelization
    - dekhn 5y ago
      both are very interesting both from a chemistry standpoint as well as a tasty standpoint.
- csense 5y ago
  I never got far enough in chemistry to really figure out if it has explanatory or predictive power. If you ask a CS grad "What will happen if you run this program?" they should be able to predict it. If they've gone through nand2tetris they can explain it all the way -- compiler, OS, machine language, ALU / registers / bus, logic gates. If you ask a chemistry grad "What happens when you apply heat to this molecule?" can they predict it? Can you explain it all the way -- from molecules to atoms to electrons to quantum fields? If we can't predict "Okay this is what will happen if I mix these two substances together," how do we have a good scientific theory? I guess chemistry says we always end up with the same atoms we started with (unless you start to go nuclear by using energetic particles to modify the nucleus), but can we predict which of the zillions of possible rearrangements will actually happen? We know by experiment that H2SO4 is an acid, and that H2SO4 is a "legal" molecule in a way that HSO3 or H5S7O9 are not. Is there a way to figure this out from first principles? Can you figure out by inspecting the chemical formula that H2SO4 will be an acid if you didn't already know that ahead of time? Can you figure out that H2SO4 will be a "legal" molecule but H5S7O9 will not? Can you look at a reaction and tell whether it will "compile" and what it does, the same way you can look at a program and figure out if it will compile and what it does? If you can't, why not? And what use is a theory of chemistry that can't make concrete predictions? If you just have a list of known substances and reactions, is that even a theory, or is it just experimental data?
  - opportune 5y ago
    Computational chemistry answers some of these questions. When you look at just a molecule by itself “what happens if you apply heat” is somewhat simple. Covalent bonds just break because the molecule is vibrating too much - think of a covalent bond as a flexible strut, if you put too much pressure on it, it snaps. This can result in the temporary formation of unstable molecules that then recombine. You could predict which particular bonds in a molecule are unstable based on the total structure, angles, electronegativity, polarity, etc. But of course those small unstable molecules can further breakdown, react with each other, and react with the parent molecule to form new stuff. So basically the parent molecule is part of some huge “power set” of potential molecules all interacting with each other.
  - 5y ago
aassddffasdf 5y ago
Exactly.

arcticfox 5y ago

Yeah, unlike https://thispersondoesnotexist.com/ https://thispersondoesnotexist.com/, this could really use a small About section or ? to hover over. Either they do something clever to exclude real molecules, my understanding of chemistry is too limited (100% possible), or it's more like "this molecule might not exist"...

dexwiz 5y ago
More likely it’s not stable or no way to synthesize it. Complex molecules have internal “stress” that needs to be weaker than the individual bonds. Making explosives is often maximizing that stress while still making a viable molecule, kind of like a mouse trap.
- semi-extrinsic 5y ago
  Nah. These are all predominantly branched and/or cyclic carbon chains, with a few heteroatoms scattered in for effect. They probably burn well, they might smell nasty, but they are not going to be explosive. Explosives (or "energetic materials" as they are known in the trade) are generally all about stuffing as many nitrogen and oxygen atoms as possible into your molecule; take TriNitroToluene as an example, it has 7 carbons, 3 nitrogens and 6 oxygens, and that's fairly mild. What these structures remind me most of is what you would find in a sour heavy crude oil. In fact, I can guarantee the person who named this website has never looked at high resolution mass spectroscopy analysis (like an FTICR-MS) of any type of petroleum, or they would have named it "this chemical is probably being pumped out of the ground right now".
  - dexwiz 5y ago
    Yes, practically this means shoving as many nitro groups together. But what makes nitro groups explosive to begin with? From what I remember, the large electron shells of the oxygen atoms repel each other, increasing the bond N-O-N angle by a few degrees. It's very easy to break these stressed bonds, and oxidize another carbon compound with the liberated oxygen, creating CO2 gas (the explosive bit). Some of the most powerful explosives are made by attaching nitro groups to stressed ring or cage structures.

t3po7re5 5y ago

For a quick check they could run the generated compounds through these databases Zinc15 - https://zinc15.docking.org/ https://zinc15.docking.org/ Chembl - https://www.ebi.ac.uk/chembl/ https://www.ebi.ac.uk/chembl/ Also as an aside I believe there's a current trend to generate chemical compounds by creating SMILES strings using BERT which is a cool way to incorporate language and chemistry (An example of a team doing that https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6 https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6)