[HN Gopher] This Chemical Does Not Exist
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This Chemical Does Not Exist
Author : optimalsolver
Score : 81 points
Date : 2021-06-28 15:32 UTC (7 hours ago)
(HTM) web link (www.thischemicaldoesnotexist.com)
(TXT) w3m dump (www.thischemicaldoesnotexist.com)
| iskander wrote:
| First one I pulled up I recognized as actually existing. Seems
| like they need a blacklist of real chemicals?
| Aperocky wrote:
| Should rename to 'This Chemical Might Exist'
| pama wrote:
| Previous submission with comment from creator is here:
| https://news.ycombinator.com/item?id=26937223
| prirai wrote:
| Duplicate..seriously? Was posted two months ago here:
| https://news.ycombinator.com/item?id=26937223
| gus_massa wrote:
| From the FAQ:
|
| > _Are reposts ok?_
|
| > _If a story has not had significant attention in the last
| year or so, a small number of reposts is ok. Otherwise we bury
| reposts as duplicates._
|
| It's intentional unclear what significant attention means, but
| the last submission has (3 points | 64 days ago | 3 comments)
| that is not very significant.
| [deleted]
| mensetmanusman wrote:
| If it has never been made, does it exist if the pathway does
| actually exist?
| jhbadger wrote:
| 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?
| t3po7re5 wrote:
| For a quick check they could run the generated compounds
| through these databases Zinc15 - https://zinc15.docking.org/
| 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)
| happytoexplain wrote:
| 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 wrote:
| 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...
| csense wrote:
| 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 wrote:
| 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.
| permo-w wrote:
| the Maillard Reaction?
| CrazyStat wrote:
| The Maillard reaction is protein browning,separate from
| sugar caramelization
| dekhn wrote:
| both are very interesting both from a chemistry
| standpoint as well as a tasty standpoint.
| arcticfox wrote:
| Yeah, unlike 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 wrote:
| 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 wrote:
| 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".
| tyingq wrote:
| They return PDB format files for molecules:
|
| https://www.thischemicaldoesnotexist.com/molecule.pdb
|
| There appear to be several repositories of this format. Maybe
| they just randomly generate until they find one with a hash
| that doesn't exist? (Though it's not clear to me how much
| order of the lines in the format matters).
| polynomial wrote:
| I'm not a professional chemist, but I'm pretty sure Hydrogen
| exists: https://i.imgur.com/X1Lo62h.png
| diplodocusaur wrote:
| I got a lone Hydrogen atom
| slyrus wrote:
| Hmm... first molecule I got is in pubchem as cpd 5216868. I guess
| the space of possible molecules with under, say, 25 heavy atoms,
| while large, is much smaller than that of possible faces.
| trutannus wrote:
| I noticed a pharmaceutical come up a little while back when I
| tried this out myself. Maybe a better name would be "This
| Chemical May Not Exist".
| pmoriarty wrote:
| I'd like to see a "This Chemical Is Not What You Think It Is"
| site, that explains what chemicals like the infamous dihydrogen
| monoxide really is.
| canadianfella wrote:
| What would be the content other than a simple joke?
| sedeki wrote:
| Sounds like a dangerous chemical. Luckily we have stuff with
| electrolytes.
| gotostatement wrote:
| its what plants crave!
| a1369209993 wrote:
| It also frequently contains deuterium hydroxide, a chemical
| used in nuclear reactors and the manufacture of thermonuclear
| bombs.
| aazaa wrote:
| That's an interesting way to phrase it. I get that this is a play
| off of the "This X doesn't exist.", where X is a machine-
| generated entity such as a picture of a cat or the bio for a
| person.
|
| If by "chemical" you mean "substance (as represented by this
| molecule)" and if by "exist" you mean "hasn't been made yet,"
| then it might make sense.
|
| "This substance (as represented by this molecule) has not been
| made yet" doesn't have the same ring to it, though.
|
| Molecules are abstractions. Leaky ones at that.
| nom wrote:
| Now someone get thisphotodoesnotexist.com and show an image of
| random pixels.
| slenk wrote:
| Is there a significance of this molecule?
| [deleted]
| TheCapn wrote:
| Well, it seems to be generated randomly; similar to the "this
| person does not exist" site(s)
|
| https://www.thispersondoesnotexist.com/
| slenk wrote:
| I missed that it changed
| _Nat_ wrote:
| Guessing that site's showing composite-images?
|
| Many of the images seem reasonable. They can have odd
| asymmetries that may give an unnatural vibe, though most
| don't seem to have majorly overt issues.
|
| Most of the more overt issues seem to be melding facial wear
| (like glasses and ear-rings) into skin.
|
| The most overt oddity was a woman with " _stuff_ " splattered
| on her face.. I'd be curious how/why that'd be something that
| could be generated..
|
| A lesser oddity was a man who had a mustache that appeared to
| be shaven on one half, but not the other.
| FeepingCreature wrote:
| It's not composite any more than human imagination is
| composite. It's based on existing images, but only in the
| sense that they formed a basis for learning how a human
| face generalizes.
| tiborsaas wrote:
| It's using generative adversarial networks create these
| images from a model.
|
| Well explained here:
| https://www.youtube.com/watch?v=SWoravHhsUU
| hypertele-Xii wrote:
| (It changes every time you refresh the page)
| slenk wrote:
| Ahh I missed that
| Jeff_Brown wrote:
| I understand why "This person does not exist" is interesting.
| Generating a fake person seemed hard until we could do it.
|
| But why is this interesting? Minus the animation, isn't this
| something any smart high-schooler could do with pen and paper?
| jyriand wrote:
| I think the hard part is that you can't draw something that
| already exists
| skohan wrote:
| Is it guaranteed not to exist? I would have assumed the
| interesting part is that these obey the laws of chemistry.
| But even then it seems like you could do something fairly
| simple algorithmically to achieve this.
| Jeff_Brown wrote:
| Yeah, it seems like the only way to guarantee it doesn't
| exist (rather than that it simply hasn't been catalogued)
| would be to draw something impossible -- which seems less
| interesting than drawing something possible.
| skissane wrote:
| > Minus the animation, isn't this something any smart high-
| schooler could do with pen and paper?
|
| Our 8 year old does this with pen and paper, and sometimes also
| with some website that lets you draw molecules (there's a few,
| forget which one(s) he uses). That said, his molecules aren't
| always possible (he understands valence but sometimes he makes
| mistakes with it or just stops caring about it).
| libria wrote:
| Heh, just found out there's one for numbers
| https://thisnumberdoesnotexist.com/
| tyingq wrote:
| It did reliably generate numbers that produced zero google
| search results. Maybe that's what they meant?
|
| Though it did also occasionally spit out a "number" with a
| letter in it, like "q29199.951301068788".
| Jeff_Brown wrote:
| I just laughed for a full thirty seconds.
|
| What's most interesting about that is somebody actually
| bothered to put it together.
| m3kw9 wrote:
| This Chemical Probably Does Not Exist
| IBCNU wrote:
| Somebody hook this up to a 3d bio printer thing... that'll go
| well right?
| parsecs wrote:
| Not sure if the "3d bio printer thing" that you're thinking of
| can synthesize stuff at the molecular level though. Maybe it
| would be fun to have it print scale models of the chemicals
| with colored filament.
| ampdepolymerase wrote:
| If you can find an efficient, generic, and universal method
| for synthesizing molecules of arbitrary shape and complexity,
| then you would receive the Nobel Prize for Chemistry and
| possibly Physics and Medicine too. You would also likely
| receive the Turing award (if your method is algorithmic and
| not using ML blackboxes since the search space for
| biochemistry is absolutely immense) and there may be entire
| prizes named after you.
|
| Whoever can find such an algorithm will put Corey and
| Woodward out of a job and the entire field of organic
| chemistry will study your name and life in future.
| diogenesjunior wrote:
| Many of the chemicals generated actually do exist.
| honie wrote:
| It appears that the molecules on the page are generated with a
| machine learning algorithm trained on a small organic molecules
| dataset that is heavily biased towards cyclic, particular
| nitrogen heterocyclic, structures (I only sampled about 40 of
| them, so it could also have just been my luck).
|
| The model seems to have learnt chemistry pretty well because, as
| many have already pointed out, most of the molecules generated do
| actually exist (or are extremely likely accessible if they
| haven't already been documented). Even the ones with strange bond
| angles have otherwise perfectly normal number of bonds. The only
| time where I get molecules that cannot possibly exist are those
| with overlapping atoms that just defy known physics.
|
| Addendum: it is worth noting that the model might actually have
| been trained with data that contain bond lengths, or even spatial
| information _if no post-generation geometry optimisation is
| performed before a molecule is rendered_.
| whymauri wrote:
| For demos like this, it's pretty common to just run RDKit for a
| structural check before serving the user the actual chemical. I
| don't know what kind of model this is, though.
|
| They could have limited SMILES (popular choice) to have a more
| stable generative space or they might have introduced validity
| into the loss. I think the coolest part is how the builder got
| all the rendering to work well!
|
| Or it could also be a rule-based fragment model guaranteed to
| hit a valid structure, that works too.
| isoprophlex wrote:
| I did exactly this once: trained a simple language model
| (Karpathy's Char-RNN iirc) on a txt file with SMILES strings.
|
| After validating the output, it was easy to plot a (2D)
| skeletal formula. I never got around 3D renders, but I guess
| a SMILES -> 2D -> 3D pipeline with some molecular mechanics
| structure energy minimization for the 3D part is cheap to do.
|
| I found the output surprisingly diverse. Model was very good
| in adding branched lipid tails that kept rambling on forever,
| though...
| messe wrote:
| So https://thischemicalprobablyexists.com might be a better
| title?
|
| I'm not a chemist, I've an undergrad degree in
| physics/mathematics. Intuitively, your answer sounds right, but
| I'm not in a position to judge for sure.
| bee_rider wrote:
| Chemistry is just the integral of physics (he said, extremely
| sophomoricly), so you should be able to work it out.
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(page generated 2021-06-28 23:00 UTC)