reagent table organic synthesis

Building a Reagent Table for Organic Synthesis: From Reaction Sketch to Bench-Ready List

Build a reagent table for organic synthesis: equiv, mmol, mass, volume columns. Worked Suzuki example. Spreadsheet vs ELN vs dedicated tool trade-offs.

ChemStitchMay 28, 2026

Every literature procedure compresses into a one-line condition string — “Pd(PPh₃)₄ (5 mol%), Na₂CO₃ (2.0 equiv), DME/H₂O, 80 °C, 12 h”. To run it, you expand that into a reagent table: every reagent on a row, with MW, equivalents, mmol, mass or volume, and any notes. The reagent table is the document that bridges literature procedure and bench execution. Every lab notebook entry for a synthesis starts with one, and most synthesis-related errors trace back to a reagent table that was incomplete or wrong.

This post walks through what columns a reagent table contains, the order to fill them in, a worked example for a Suzuki coupling, and the trade-offs between handwritten tables, spreadsheets, and integrated tools.

What a reagent table contains

A practitioner reagent table has, at minimum, these columns:

Reagent name — the form on the shelf (free base, salt, hydrate). Generic name + structure is fine; CAS number is sometimes added for traceability.
MW (molecular weight, g/mol) — for the form on the shelf.
Density (g/mL) — for liquid reagents only. Required to convert mass to volume.
Equiv (equivalents) — the practitioner-facing input. The limiting reagent is 1.0 equiv; everything else is relative.
mmol (millimoles) — derived from equiv × scale.
Mass (mg or g) — derived from mmol × MW.
Volume (µL or mL) — for liquids, derived from mass / density.
Notes — purity, salt form, hygroscopic flag, hazard, supplier lot number.

For solutions (reagents in solvent, like 2.5 M n-BuLi in hexanes), you add a concentration column and derive volume from mmol / concentration. For gases (e.g., H₂ in a Parr shaker), the table records pressure or balloon volume rather than mass.

The order to fill the table in

Practitioner workflow goes top-to-bottom in equiv-first order. The literature procedure already gives you the equiv numbers; the rest is arithmetic.

Workflow

Step 1: pick scale (mmol of limiting reagent). Step 2: enter equiv for each reagent from the literature procedure. Step 3: calculate mmol = equiv × scale. Step 4: calculate mass = mmol × MW / 1000 (in grams). Step 5: for liquids, calculate volume = mass / density.

The two derived formulas:

Key formulas $\text{mmol} = \text{equiv} \times \text{scale (mmol of LR)}$ $\text{mass (mg)} = \text{mmol} \times \text{MW (g/mol)}$ $\text{volume (mL)} = \frac{\text{mass (g)}}{\text{density (g/mL)}}$

For liquids delivered as solutions, the volume comes from concentration instead of density: volume = mmol / molarity. The molarity calculation post covers the molarity setup for stock solutions.

Worked example — Suzuki coupling reagent table

A typical first-pass Suzuki coupling protocol:

Aryl bromide (1.0 equiv), arylboronic acid (1.2 equiv), Pd(PPh₃)₄ (5 mol%), Na₂CO₃ (2.0 equiv), DME/H₂O (4:1, 0.2 M), 80 °C, 12 h.

At 2.0 mmol scale of the aryl bromide:

Worked Example — Suzuki coupling at 2.0 mmol scale

Reagent	MW	Density	Equiv	mmol	Mass / Volume
4-bromobiphenyl (LR)	233.1	— (solid)	1.0	2.0	466 mg
Phenylboronic acid	121.9	— (solid)	1.2	2.4	293 mg
Pd(PPh₃)₄	1155.6	— (solid)	0.05 (5 mol%)	0.10	116 mg
Na₂CO₃	105.99	— (solid)	2.0	4.0	424 mg
DME (solvent)	90.12	0.868	—	—	8.0 mL
H₂O (solvent)	18.02	1.00	—	—	2.0 mL

Solvent total: 10 mL (DME/H₂O 4:1, giving reaction concentration = 2.0 mmol / 10 mL = 0.20 M, matching the protocol).

The catalyst row uses mol% (5%) which expands to 0.05 equiv; the underlying arithmetic is the same as for any other reagent. The limiting reagent post covers when the substrate is the limiting reagent (almost always, by convention) and the rare cases when it isn’t.

The columns that get skipped — and the errors that follow

Reagent tables built quickly tend to skip the columns that protect against the most common errors:

Density column for liquids. Skipping it means converting volume to mass mentally (or assuming density = 1.0 for organic solvents, which is wrong for DCM (1.33), CHCl₃ (1.49), and most halogenated solvents). The volume of a liquid reagent should always come from the formula volume = mass / density, never from eyeballing.
Salt form / purity in notes. A table with “piperidine” in the name column and MW 85.15 reads correctly — until the bottle on the shelf is piperidine HCl (MW 121.61). Recording the form prevents this.
Solvent volume. Many tables include only the substrate / reagents / catalyst rows and omit solvent. Then the reaction concentration drifts: a 2 mmol reaction in “a few mL of solvent” might end up at 0.05 M or 1.0 M, both of which can change selectivity. Always record solvent volume and back-compute reaction concentration.
Reaction concentration row. Calculated from limiting reagent mmol / solvent volume; flags whether you’re in the typical 0.1–0.5 M window or have drifted toward dilute (0.01 M, used for macrocyclization) or concentrated (1–5 M, used for some couplings).

Common Mistake

Liquid reagent volumes calculated as if density = 1.0 g/mL. For dichloromethane (density 1.33), the “1 mL” you wanted to pipette by mass is actually 0.75 mL by volume — a 25% error. Pipette by volume, not by mass; or, if you must weigh, divide mass by the actual density.

Spreadsheet, ELN, or dedicated tool?

Three places practitioners build reagent tables:

Spreadsheet (Excel / Google Sheets). Most common in academic and small biotech labs. Pro: free, customizable, shared across lab via a group file drive. Con: formula errors propagate silently (a wrong cell reference in row 3 can shift all downstream calculations), version drift between users, and no structure-to-MW link. The LibreTexts How to be a Successful Organic Chemist reagent-table chapter covers the spreadsheet approach in detail.
ELN (Dotmatics, Benchling, BIOVIA, Signals Notebook). Enterprise-grade, integrated with the experiment record. Pro: traceability, lot numbers, search across past experiments. Con: per-seat licensing, workflow-heavy for small reactions, and onboarding overhead. Practical for established pharma / biotech with an IT budget; overkill for academic labs and most small biotechs.
Dedicated stoichiometry tool. Lighter than ELN, faster than spreadsheets, and (if integrated with structure drawing) auto-populates MW from drawn structures. The ChemStitch stoichiometry calculator takes a drawn reaction or pasted SMILES, pulls MW from each structure, and builds the reagent table on equiv input.

The decision usually comes down to whether you already have an ELN deployed: if yes, build the table there for traceability; if no, a dedicated tool gives most of the benefit without the procurement cycle.

After the reaction — closing the loop on yield

The reagent table is half the document; the other half is the yield calculation after workup. Once you weigh the purified product, you back-compute percent yield from the theoretical yield (mmol of limiting reagent × MW of product). The percent yield post covers the calculation and the most common reasons real yield falls short of theoretical. For multi-step syntheses, the cumulative yield post walks through how individual step yields multiply across a route.

A calculator that builds the table

The reagent table workflow is mechanical once you know the equiv numbers — but mechanical with enough columns that errors slip in if you do it by hand. The stoichiometry calculator on ChemStitch builds the full table from a drawn reaction (or pasted SMILES for the limiting reagent), auto-fills MW from the structure, accepts equiv (or mol% for catalysts), and outputs the bench-ready mass / volume / mmol columns with form, purity, and salt-form corrections in the notes. For the limiting-reagent decision itself, see limiting reagent calculations; for the equiv-first framing that drives the table, see equivalents in organic chemistry.