Reaction mechanisms, drawn on real structures
Most mechanism diagrams are drawn with R groups and a general case. These are run on the molecules you give them, step by step, with the curly arrows resolved to actual atoms — and each one states what it assumes and what it is not claiming.
A mechanism on this site is a sequence of elementary steps. Each step is a small reaction in its own right, so it is run the same way a whole reaction is run: on your structures, producing a real intermediate you could in principle isolate, and checked to make sure the sequence actually arrives at the product. A pathway that does not arrive is not shown at all.
That check is the reason this list is short. We would rather carry twenty-six classes correctly than generate a plausible drawing for every reaction anyone asks about. Where a class is not covered, the page says so in those words instead of improvising.
Every mechanism that is written
Nucleophilic acyl substitution
3 steps
The nucleophile adds to the carbonyl, the carbon holds four groups for a moment, and the leaving group is pushed out as the double bond comes back.
Bimolecular nucleophilic substitution
1 step
One step. The nucleophile comes in on the opposite side from the leaving group, and the carbon turns inside out as the exchange happens.
Imine formation
3 steps
The amine adds to the carbonyl, the resulting alcohol-amine loses water, and a carbon–nitrogen double bond is left.
Diels-Alder cycloaddition
1 step
One step. Six electrons move round a ring at once, two new single bonds form at the ends and the double bond ends up in the middle.
Bimolecular elimination
1 step
One step. The base takes a hydrogen from one carbon while the leaving group departs from the next, and a double bond forms between them.
Unimolecular nucleophilic substitution
3 steps
The leaving group goes first, on its own, leaving a flat carbon with a positive charge. Whatever is around then attacks it from either side.
Organometallic addition to a carbonyl
2 steps
The carbon attached to the metal is nucleophilic. It adds to the carbonyl, and the alkoxide that results is protonated when the reaction is worked up.
Diels-Alder with an aromatic diene
1 step
The same six electrons moving round at once, except that the diene is an aromatic ring and gives up its aromaticity to react.
Electrophilic aromatic substitution
2 steps
The ring gives up its aromaticity for one step to attack the electrophile, then loses a proton to get it back.
Epoxide opening under base
3 steps
A base makes the nucleophile, the nucleophile attacks the less crowded end of the ring, and the strained ring springs open.
Wittig olefination
3 steps
The ylide adds to the carbonyl, the four-membered ring that results falls apart the other way, and the phosphorus leaves with the oxygen.
Aldol condensation
4 steps
A base makes the enolate, the enolate attacks the other carbonyl, and the alcohol that results loses water to leave a conjugated enone.
Unimolecular elimination
3 steps
Acid turns the hydroxyl into a good leaving group, it leaves on its own, and the cation then loses a proton to give the alkene.
Epoxide opening under acid
3 steps
Acid protonates the ring oxygen, which stretches the bond to the carbon that can best hold a positive charge, and the nucleophile attacks that one.
Reductive amination
4 steps
The amine and the carbonyl condense to a C=N, and the reducing agent then delivers a hydride to that carbon. The order matters: nothing reduces the carbonyl itself.
Acid removal of a Boc group
3 steps
Acid protonates the carbamate, the tert-butyl group leaves as a cation because it can, and what is left gives off carbon dioxide to free the amine.
Heck coupling (catalytic cycle)
4 steps
The metal inserts into the aryl-halide bond, the alkene inserts into the aryl-metal bond, the metal takes back a hydrogen and leaves, and a base strips it so the metal can start again.
Base removal of an Fmoc group
3 steps
The base takes a hydrogen the fluorene ring makes unusually acidic, the carbamate is pushed out, and what is left gives off carbon dioxide.
Fluoride removal of a silyl group
2 steps
Fluoride attacks the silicon, which is where it would rather be than anywhere else, and the alcohol is released.
Conjugate addition
3 steps
A base makes the enolate, and it adds to the far end of the enone rather than to the carbonyl. The charge travels through the double bond to the oxygen and then comes back as the product is protonated.
Suzuki coupling (catalytic cycle)
3 steps
The metal inserts into the aryl-halide bond, the boron hands over its carbon, and the two groups on the metal join and leave together.
Sonogashira coupling (catalytic cycle)
4 steps
The metal inserts into the aryl-halide bond, the alkyne loses its hydrogen and is carried across, and the two groups join and leave together.
Amide coupling through an active ester
4 steps
The reagent turns the acid into something an amine will attack, and then it is an ordinary acyl substitution: attack, tetrahedral intermediate, collapse, proton transfer.
Amide coupling through an O-acylisourea
4 steps
The reagent turns the acid into something an amine will attack, and then it is an ordinary acyl substitution: attack, tetrahedral intermediate, collapse, proton transfer.
Buchwald-Hartwig amination (catalytic cycle)
3 steps
The metal inserts into the aryl-halide bond, the amine takes the halide's place on the metal and loses its proton to the base, and the two groups join as the metal lets go.
Acid-catalysed hydration of an alkene
3 steps
Acid gives the alkene a proton, leaving a positively charged carbon; water attacks it and then loses a proton, and the acid is returned.
What a mechanism page will and will not tell you
It will tell you which bond breaks, which forms, and which only changes order, and the words always match the drawing. It will tell you what the drawing assumes, and which other pathways the class is known to run by.
It will not tell you that this is what happened in your flask. Nothing on these pages is evidence. If you want evidence, the reaction records are the other half of this library: experiments somebody actually ran, with the conditions they used and a source you can check.
Questions people ask
Are these mechanisms experimentally proven for my substrate?
No, and the pages say so on every screen. A mechanism here is the pathway taught for its class, run on the structures you supply. It is rule-derived. What is evidence is the reaction record — what was mixed, under what conditions, and what came out — and that is kept separate and labelled differently.
Why do some reactions show no mechanism at all?
Because none has been written for that class, or because the written one does not reach the product from those structures. A pathway that does not arrive is not that reaction's pathway, so nothing is shown. Refusing is the intended behaviour: a smaller set of families carried correctly is worth more than a plausible-looking drawing for everything.
Why is hydrogenolysis missing?
It happens on a metal surface. Arrow pushing describes electrons moving between orbitals in solution, and drawing a Cbz deprotection that way would teach something false in order to fill a gap in a table.
Where do the curly arrows come from?
Each step declares its arrows in its own map numbers, and they are resolved to real atoms when the step runs on your substrate. They are drawn by the same component that draws the structures, so an arrow always points at the atom it is about rather than at the place that atom sat in the first frame.
Do the steps tell me how fast the reaction goes?
No. Every step is given the same time on screen because the animation gives every step the same time, not because they take the same time in a flask. Where relative speed is part of the pathway — a proton transfer against the attack it follows — it is said in words in the assumptions, which is the only place we are entitled to say it.