Jacs Methods

---
name: jacs-methods
description: Use when checking synthesis and characterization rigor for a Journal of the American Chemical Society (JACS) manuscript — purity, NMR/HRMS/IR/UV-vis, elemental analysis or HPLC, single-crystal X-ray/CCDC, and catalysis controls/mechanism/kinetics. Audits experimental rigor — it does not write narrative or polish prose.
---

# Synthesis and Characterization Rigor (jacs-methods)

## When to trigger

- New compounds are reported and you must confirm full characterization
- A reviewer could ask "is this compound pure?" or "where is the X-ray?"
- A mechanism is claimed but only proposed, not tested
- Catalysis scope/selectivity is reported and controls are unclear

## Characterization rigor by claim type

JACS requires that **claims are fully supported by characterization data and
appropriate controls**. Match the data package to what you assert.

### Every new, isolable compound

- [ ] **¹H NMR** — solvent, field; δ (ppm), multiplicity, J (Hz), integration
- [ ] **¹³C{¹H} NMR** — all resolvable carbons (note coincident peaks)
- [ ] Heteronuclear NMR as relevant: **¹⁹F**, **³¹P**, **¹¹B**, etc.; 2D for assignment
- [ ] **HRMS** — ionization mode, calcd vs found m/z for the assigned formula
- [ ] **IR** — diagnostic bands (C=O, N–H, C≡N, M–CO, etc.) when structurally informative
- [ ] **Purity evidence** — at least one of: CHN(S) elemental analysis (calcd vs found, typically within accepted tolerance), or HPLC/GC purity, plus clean NMR
- [ ] Melting point / optical rotation / UV-vis as appropriate to compound class

### Stereochemistry / chirality

- [ ] **ee** by chiral HPLC/GC/SFC (column, eluent, flow, detector; report racemate trace)
- [ ] **dr** by NMR or HPLC; specify how measured
- [ ] Absolute configuration assigned (X-ray, VCD, comparison to known, or derivatization) — state the method

### Solid-state structure

- [ ] **Single-crystal X-ray** for structurally pivotal claims; deposit CIF with **CCDC** and cite the number
- [ ] Crystal/refinement table (formula, space group, R1/wR2, GooF, completeness)
- [ ] **checkCIF/PLATON** run; A/B-level alerts resolved or justified
- [ ] PXRD for bulk-phase identity of solids/materials

### Catalysis

- [ ] **Scope table** — representative, honest substrate range (not only easy cases); note failures
- [ ] **Control experiments** — no-catalyst, no-ligand, no-additive, radical traps/clocks as relevant
- [ ] **Mechanism** — evidence-based: kinetics (orders, rate law), KIE, labeling, intermediates (isolation/spectroscopy), Hammett, ee–ee(cat) correlation
- [ ] Catalyst loading, TON/TOF, and reproducibility (replicate runs) reported
- [ ] Metal/ligand source, purity, and any trace-metal control where relevant

### Materials / physical

- [ ] Composition and phase: PXRD, EDX/XPS, ICP, TGA, BET as appropriate
- [ ] Morphology with **scale bars** and representative-vs-statistical imaging (SEM/TEM/AFM)
- [ ] Property measurement with method, conditions, and error/replication
- [ ] Spectroscopy (UV-vis/PL/Raman/EPR/electrochemistry) tied to the claimed property

### Computation (if used to support mechanism/structure)

- [ ] Functional, basis set/pseudopotentials, solvation model, software + version
- [ ] Stationary points characterized (frequencies; TS has one imaginary mode)
- [ ] Optimized coordinates (xyz) deposited in SI; energies referenced consistently

## Reproducibility test

Could an independent chemist reproduce each yield, ee, and spectrum from the
written procedure alone? If not, the procedure is incomplete — fix before figures.

## Anti-patterns

- New compound reported with no purity criterion (no EA, no HPLC, no clean ¹³C)
- "Pure by NMR" as the only purity statement for a key compound
- Mechanism drawn as a cycle with no kinetic/labeling/control support
- Crystal structure shown but CIF not deposited / no CCDC number
- Scope table that hides failed substrates; idealized yields not reproducible
- HRMS reported without ionization mode or calcd/found pair

## Output format

```
【Compounds】N new; full characterization complete for [ ] / missing for [...]
【Purity basis】EA / HPLC / clean NMR — per compound
【Stereochem】ee/dr method + absolute config method (if chiral)
【X-ray】CCDC # [...]; checkCIF clean? Y/N
【Mechanism】claimed = [...]; evidence = [kinetics/KIE/labeling/controls]
【Reproducible from text?】Y/N — gaps: [...]
【Next】jacs-figures → jacs-supplementary
```

## Related resources

- [`../../resources/external_tools.md`](../../resources/external_tools.md) — instruments, CCDC/PDB deposition, crystallography and computational software