Every reaction the engine can perform
Each of these is a rule the platform applies to your structures: what bonds have to be there, what they become, and what has to be in the flask for it to run at all. They are the vocabulary behind every predicted outcome.
A transformation is written as a pattern, not as an example. "Fischer esterification" is not a particular acid and a particular alcohol — it is the statement that a carboxylic acid and an alcohol under acid give an ester and water, and it applies to whichever acid and alcohol you bring.
What makes these usable rather than decorative is the conditions attached to each. A rule that fires on anything shaped correctly would propose oxidations with no oxidant and couplings with no catalyst. These say what they need, and withhold themselves when it is not there.
Substitution
Substitution by an anionic nucleophile
mechanism
An anion displaces the halide from the back, turning the carbon over.
Epoxide opening under acid
mechanism
An acid protonates the epoxide oxygen, and the ring opens at the carbon better able to carry positive charge — the more substituted one.
Epoxide opening under base
mechanism
With no acid to open the ring first, the nucleophile has to attack it directly, so it goes to the carbon that is easier to reach — the less substituted one.
Solvolysis of a crowded halide
mechanism
A crowded carbon lets its leaving group go before anything arrives. The flat intermediate is then attacked from either face, so any configuration it had is lost.
Alkylation of an amine
mechanism
An amine attacks an alkyl halide and takes its carbon, becoming a more substituted amine.
Alkylation of a thiol
mechanism
A thiol or its anion attacks an alkyl halide and takes its carbon, leaving a thioether.
Mitsunobu coupling
mechanism
A phosphine and an azodicarboxylate turn an alcohol into a leaving group where it stands, and an acidic partner displaces it.
Addition
Conjugate addition
mechanism
A stabilised carbanion adds to the far end of an enone rather than to its carbonyl.
Organometallic addition to a carbonyl
mechanism
The carbon of the organometallic adds to the carbonyl carbon; the alcohol appears on work-up.
Alkene hydration
mechanism
Water adds across a double bond. The hydrogen goes to the carbon that already has more of them and the hydroxyl to the other, so the more substituted alcohol is the one that forms.
Hydroboration of an alkene
mechanism
Boron and hydrogen add across the double bond, boron to the less hindered carbon, and the carbon–boron bond is then replaced by a hydroxyl with retention. The alcohol ends up on the opposite carbon from the one acid-catalysed hydration would give.
Bromination of an alkene
mechanism
Bromine adds across the double bond. The second bromide arrives on the opposite face from the first, so the two end up anti.
Dihydroxylation of an alkene
mechanism
Two hydroxyls are delivered to the same face of the double bond, giving the cis diol.
Deprotection
Boc removed from an amine
mechanism
Acid takes the carbamate off, leaving the free amine.
Cbz removed from an amine
mechanism
Hydrogen over a metal cleaves the benzyl carbamate, leaving the free amine.
Benzyl ether removed
mechanism
Hydrogen over a metal cleaves the benzyl ether, leaving the alcohol.
Silyl ether removed
mechanism
Fluoride cleaves the silicon–oxygen bond, leaving the alcohol.
Fmoc removed from an amine
mechanism
A secondary amine takes the acidic hydrogen and the group falls away.
Demethylation of an aryl methyl ether
mechanism
The methyl is taken off an aromatic methyl ether, leaving the phenol.
Reduction
Reductive amination
mechanism
The imine forms and is reduced in the same pot, giving the amine.
Alkene hydrogenation
mechanism
Hydrogen adds across a double bond, turning an alkene into an alkane.
Reduction of an aldehyde or ketone
mechanism
Hydride adds to the carbonyl carbon, giving the alcohol.
Reduction of an ester
mechanism
The ester is taken to the primary alcohol, releasing the alcohol of the ester.
Reduction of an amide
mechanism
The carbonyl is removed entirely, leaving the amine.
Reduction of a nitro group
mechanism
A nitroarene is reduced to the aniline.
Acylation
Acyl chloride with an amine
mechanism
The amine displaces chloride from the carbonyl, giving the amide.
Acyl chloride with an alcohol
mechanism
The alcohol displaces chloride from the carbonyl, giving the ester.
Anhydride with an amine
mechanism
The amine takes one acyl group, releasing the acid of the other.
Anhydride with an alcohol
mechanism
The alcohol takes one acyl group, releasing the acid of the other.
Amide coupling with an activating reagent
mechanism
A coupling reagent turns the acid into something an amine will attack, and the amide forms. Unlike the direct condensation, this works on anilines.
Cross-coupling
Heck coupling
mechanism
Palladium inserts into the aryl-halide bond, the alkene inserts into the aryl-palladium bond, and the hydride is eliminated to leave the alkene where it started, now carrying the ring.
Suzuki coupling
mechanism
Palladium inserts into the aryl-halide bond, the boron hands its carbon to the metal, and the two organic groups are joined as the metal lets go.
Sonogashira coupling
mechanism
A terminal alkyne is joined to an aromatic ring. The alkyne loses its hydrogen to a base, copper carries it to the palladium, and the two are joined there.
Buchwald-Hartwig amination
mechanism
Palladium joins an amine to an aromatic ring, on rings that are not activated and would not react on their own.
Copper-catalysed ether coupling
mechanism
Copper joins an alcohol or a phenol to an aromatic ring that would not accept it on its own.
Acid–base neutralisation
Neutralisation of a hydrohalic acid by a metal hydroxide
mechanism
The acid gives its proton to the hydroxide ion. The proton and the hydroxide become water, and the remaining ions form a salt.
Neutralisation of an oxyacid by a metal hydroxide
mechanism
An acid whose proton sits on an oxygen (such as nitric or sulfuric acid) transfers that proton to hydroxide, giving water and the corresponding salt. Polyprotic acids lose one proton per step.
Neutralisation of a carboxylic acid by a metal hydroxide
mechanism
A carboxylic acid gives its acidic proton to hydroxide, forming water and a carboxylate salt.
Cyclocondensation
Ring closure to a pyrazole
mechanism
The free nitrogen of a hydrazone closes onto the carbonyl three atoms away, and the ring loses water to become an aromatic pyrazole.
Ring closure to an isoxazole
mechanism
The same closure with the oxygen of an oxime in place of the second nitrogen, giving an isoxazole.
Ring closure to a pyrrole
mechanism
The nitrogen of an imine formed at one end of a 1,4-dicarbonyl closes onto the other carbonyl, losing water to give a pyrrole.
Electrophilic aromatic substitution
Electrophilic aromatic halogenation
mechanism
A halogen replaces a hydrogen on an aromatic ring, releasing the hydrogen halide.
Friedel-Crafts acylation
mechanism
A Lewis acid pulls the halide off an acyl halide, and the aromatic ring attacks the acyl group. The groups already on the ring decide which carbon reacts.
Friedel-Crafts acylation with an anhydride
mechanism
The same reaction with an anhydride as the acyl donor, releasing the carboxylic acid.
Elimination
Alcohol dehydration
mechanism
An alcohol loses water to give an alkene. The more substituted alkene is the one that forms.
Elimination with a small base
mechanism
The base takes a hydrogen next to the leaving group. A small base reaches the more crowded position, so the more substituted alkene forms.
Elimination with a bulky base
mechanism
A bulky base cannot reach the crowded hydrogen, so it takes one from the least hindered position and the less substituted alkene forms.
Oxidation
Primary alcohol to the aldehyde
A primary alcohol is taken to the aldehyde and no further.
Primary alcohol to the acid
mechanism
A strong oxidant carries a primary alcohol past the aldehyde to the carboxylic acid.
Secondary alcohol to the ketone
mechanism
A secondary alcohol gives the ketone, which cannot be oxidised further without breaking a bond.
Acid–carbonate
Hydrogencarbonate salt with a strong acid
mechanism
The acid protonates hydrogencarbonate. The resulting carbonic acid falls apart into water and carbon dioxide, which is why the mixture fizzes.
Hydrogencarbonate salt with a carboxylic acid
mechanism
A carboxylic acid (vinegar, for example) protonates hydrogencarbonate (baking soda), giving a carboxylate salt, water and carbon dioxide.
C-H functionalisation
Aromatic C–H borylation with a diboron reagent
mechanism
A diboron reagent replaces an aromatic hydrogen, giving the aryl boronate and one equivalent of the boron–hydrogen reagent.
Aromatic C–H borylation with a boron–hydrogen reagent
mechanism
A boron–hydrogen reagent replaces an aromatic hydrogen, giving the aryl boronate and hydrogen.
Cycloaddition
Diels–Alder cycloaddition
mechanism
A diene and an alkene join at both ends at once, making a six-membered ring with one double bond left in the middle.
Diels-Alder with an aromatic diene
mechanism
A five-membered aromatic ring with one oxygen or nitrogen acts as the diene and adds across an alkene, giving a bridged bicyclic adduct.
Nucleophilic aromatic substitution
Nucleophilic aromatic substitution by an amine
mechanism
An amine displaces a halide from an aromatic ring that is pulled on hard enough to accept it: one carrying a nitro group opposite or beside the halide, or a ring with a nitrogen of its own.
Nucleophilic aromatic substitution by an alcohol or thiol
mechanism
An alcohol, a phenol or a thiol displaces a halide from a ring that is pulled on hard enough to accept it.
How these are kept honest
Every transformation is checked against reactions with a known answer before it ships: a set that asks whether the engine gets the right regiochemistry, the right chemoselectivity and the right answer when the answer is "nothing happens". It currently passes 54 of 54, alongside a blind set of 32 reactions drawn from families the engine must not confuse with one another.
Those are the numbers worth quoting. Out-of-sample top-1 accuracy — how often the single recorded product of a real experiment is our first candidate — is 55.8%, and it is a weaker guide, because several proposals are often chemically reasonable and only one was run. The questions page goes through what each number does and does not mean.
Questions people ask
What is a transformation, as opposed to a reaction record?
A transformation is a rule: a pattern of bonds that becomes another pattern of bonds. It is written once and applies to any substrate that matches it. A record is one experiment somebody ran. The rule tells you what would happen; the record tells you what did.
Why does a transformation sometimes refuse to fire?
Usually because what it needs is not present. An oxidation needs an oxidant, a Suzuki needs a transition metal, and an alcohol drawn on its own does not oxidise itself. Rather than quietly producing the product anyway, the engine reports the requirement by name.
Are the typical conditions a recommendation?
No. They are what the literature usually does, written down so you can see whether your conditions are in the ordinary range. They are not a procedure, they are not scaled to your flask, and they do not replace the primary source or a risk assessment.
Does a transformation predict yield?
No. Nothing on this platform predicts yield. The engine ranks candidate outcomes by how much documented precedent each has on substrates like yours, and reports that count rather than converting it into a number that looks like a probability.