What Goes Above and Below the Arrow in a Reaction Scheme
What goes above and below the arrow in a reaction scheme: reagents and equiv above, solvent and temperature below, yield under the product, one-pot rules.
Your PI hands back the draft SI with a single comment on Scheme 2: “I can’t tell what’s a reagent and what’s a reactant, and where are the conditions?” The structures are fine. The arrow is the problem — HATU, DIPEA, DMF, room temperature, and the yield are piled onto it in no particular order. Knowing what goes above and below the arrow in a reaction scheme is a small convention, but it decides whether another chemist can rerun your reaction from the figure alone.
The short version: reagents and catalysts go above, solvent, temperature and time go below, and the yield sits under the product. The rest of this post covers the cases where that one-liner runs out.
The default layout: above the arrow vs below the arrow
Most journals and textbooks follow the same split, even though no style guide enforces it rigidly:
- Above the arrow: reagents, catalysts, ligands, and additives, each with its amount — equivalents for stoichiometric reagents, mol% for catalysts. These are the things you weigh out or syringe in.
- Below the arrow: solvent, temperature, time, and atmosphere if it matters (N2, Ar, O2 balloon). These are the conditions you set.
- Under the product: the isolated yield, plus selectivity data where relevant (dr, ee, E/Z ratio).
Some groups put the yield under the arrow instead of under the product. Both appear in print. Pick one and keep it consistent across every scheme in the paper.
Acid + amine → amide, drawn as:
- Left of arrow: the carboxylic acid (and the amine, if it contributes a significant part of the product skeleton — see below)
- Above: HATU (1.2 equiv), DIPEA (3.0 equiv)
- Below: DMF, rt, 2 h
- Under the product: 87%
A reader can now rebuild the reagent table from the figure: 1.2 equiv of coupling reagent, 3.0 equiv of base, both relative to the limiting acid.
Reactant or reagent: deciding what goes left of the arrow
This is the question that trips people up most. The working rule: if a substantial part of a molecule’s skeleton ends up in the product, draw it as a structure. Put it left of the arrow with a plus sign, or draw it above the arrow as a structure. Small reagents that deliver one atom or a protecting group — NaBH4, mCPBA, Boc2O, TBSCl — go above the arrow as text.
The amine in an amide coupling is the borderline case. If it is a simple, purchasable amine (morpholine, benzylamine), chemists often write it above the arrow by name or formula. If it is a fragment you made three steps earlier, draw it, because the reader needs to see which structure it is.
Every reagent amount is relative to one species — the limiting reagent. If the figure shows two drawn reactants, the reader will assume the one on the far left is the reference unless you say otherwise. Our guide to calculating equivalents relative to the limiting reagent covers how those numbers are derived.
Multi-step and one-pot sequences: numbers vs letters
Two numbering conventions are easy to mix up:
- Numbered steps on one arrow (1., 2., 3.) mean sequential additions without isolating the intermediate. Example above the arrow: “1. TFA, CH2Cl2; 2. aldehyde, NaBH(OAc)3” for a Boc deprotection followed by reductive amination. The numbers tell the reader the order matters and the reagents are not all added at once.
- Lettered arrows (a, b, c) are used in long multi-step schemes where the conditions would crowd the figure. Each arrow carries only a letter, and a footnote under the scheme reads “Reagents and conditions: (a) …; (b) …”. Each letter is usually a separate step with its own workup.
If you isolate an intermediate, it gets its own arrow and usually its own compound number. Two steps can share one arrow when the crude intermediate was carried on without purification, but say so in the legend (“crude intermediate used directly”). Otherwise the reader will assume no workup happened between them.
Abbreviations and symbols that belong on the arrow
Arrow text is terse by design. The abbreviations below are standard enough that you don’t need to define them in the legend:
| On the arrow | Meaning |
|---|---|
| rt | room temperature |
| Δ or “reflux” | heat (give the temperature if it isn’t the solvent’s boiling point) |
| hν | light (state the wavelength for photochemistry) |
| −78 °C to rt | warmed from −78 °C to room temperature over the reaction |
| o/n or 16 h | overnight — prefer the actual time |
| cat. or mol% | catalytic amount; give mol% whenever you know it |
| MW | microwave heating (give the temperature and time) |
Byproducts are normally left off. You may see one written below the arrow with a minus sign (“−HCl”, “−H2O”) when the loss of that small molecule is the point of the step, such as a condensation. For the textbook treatment of these conventions, the University of Saskatchewan’s open organic text has a section on over-the-arrow notation.
Retrosynthetic arrows carry no conditions
The double-lined retrosynthetic arrow (⇒) means “is made from.” It points from the target back to precursors, and by convention it carries no reagents. What it can carry is a label naming the transform or disconnection — “amide”, “C–N”, “FGI” — so the reader knows which forward reaction you have in mind.
Mixing the two arrows is a fast way to confuse a reader. A forward arrow (→) with “HATU, DIPEA” on it pointing from the amide to the acid reads as a reaction that runs backward. If you are laying out a plan, use ⇒ throughout. Our step-by-step retrosynthesis guide walks through drawing those disconnections.
Edge cases: selectivity, conversion, and mixtures
- Diastereoselectivity and enantioselectivity go under the product next to the yield: “81%, 10:1 dr” or “76%, 94% ee”. If the ratio was measured on the crude material, say so in the legend.
- Conversion vs isolated yield: an LCMS or NMR conversion is not a yield. Label it (“85% conv.” or “NMR yield”) or reviewers will treat it as isolated.
- Regioisomer mixtures: draw the major isomer and give the ratio (“3:1 para:ortho”), or draw both with individual yields if you separated them.
- Reagent stoichiometry in mol% vs equiv: catalysts in mol%, everything else in equiv. A scheme reading “Pd(OAc)2 (0.05 equiv)” is correct but unusual — most readers expect “5 mol%”.
Making the scheme reusable outside the figure
A scheme in a PDF is an image. The same information becomes data when the reagents and conditions are attached to the reaction rather than floating as text. Reaction SMILES formalizes the same split you draw: reactants>agents>products, with reagents, catalysts and solvents in the middle field. Keeping agents distinct from reactants is what lets software (or the next chemist) tell the base from the substrate.
The structure drawings themselves still need to meet journal standards. Our post on drawing chemical structures for reports covers bond lengths, fonts, and the ACS 1996 settings that ACS journals, and many others, accept. If you have the reactants and product as SMILES, you can turn each SMILES into an editable structure and export an ACS-1996 figure to drop into the scheme. Once the scheme is final, the equivalents above the arrow feed straight into a reagent table for the bench.
Before you send the next draft back, read each arrow as if you had to run the reaction from it. It should tell you what to weigh, what solvent to use, how hot, how long, and what you got.