# Jacs Methods > 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. - Skill: `thedixitjain/jacs-methods` (Agent Skill) - Install (CLI): `npx skillmds add thedixitjain/jacs-methods` - Raw SKILL.md: https://api.skillmd.com/api/skills/thedixitjain/jacs-methods/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Research & Search - Author: thedixitjain (https://skillmd.com/u/thedixitjain) - Updated: 2026-09-08 - Page: https://skillmd.com/skills/thedixitjain/jacs-methods --- # 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 ## The SI data string (write it once, correctly) Every isolated compound gets a characterization block in the SI in the standard ACS order. A well-formed entry looks like: ``` (2R)-2-Fluoro-4-phenylbutan-1-ol (3a). Colorless oil, 158 mg (94%). [α]D²⁵ = +12.4 (c 1.0, CHCl₃). ¹H NMR (400 MHz, CDCl₃): δ 7.31–7.18 (m, 5H), 4.52 (dddd, J = 48.9, 8.1, 4.3, 3.9 Hz, 1H), ... ¹³C{¹H} NMR (101 MHz, CDCl₃): δ 141.6, 128.5 (d, JCF = 5.2 Hz), ... ¹⁹F NMR (376 MHz, CDCl₃): δ −186.3. HRMS (ESI+) m/z: [M + Na]⁺ calcd for C₁₀H₁₃FONa 191.0843; found 191.0841. 97:3 er (Chiralpak IA, 95:5 hexanes/iPrOH, 1.0 mL/min, 210 nm; tR major 14.2 min, minor 16.8 min). ``` Audit each block for: mass **and** percentage yield, physical state, every nucleus relevant to the structure, coupling constants on diagnostic multiplets, calcd/found within instrument tolerance, and the full chiral method — not just the er value. ## Referee rigor probes (pre-empt them) - "Compound **x** shows a peak at δ 1.56 — water or impurity?" → annotate residual-solvent peaks in the SI spectra copies before a referee circles them. - "Yields are single runs?" → state replicate counts for headline entries; give an average with the spread for the model reaction. - "Could adventitious metal catalyze this?" → for base-metal or 'metal-free' claims, report reagent lot ICP data or a deliberate trace-metal spike control. - "The cycle shows Ni(I)/Ni(III) — where is the evidence?" → every oxidation state drawn in a mechanism figure must trace to an EPR/UV-vis/electrochemical or kinetic observation, or be labeled as proposed. ## 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. The strongest SI procedures also state how the compound was purified (column eluent, distillation T/p), on what scale the reaction was validated, and any setup detail on which the outcome hinges (drying of solvent, exclusion of light, stirring rate for biphasic mixtures). ## 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 --- **Source:** [`brycewang-stanford/Awesome-Journal-Skills`](https://github.com/brycewang-stanford/Awesome-Journal-Skills) → `Journal-of-the-American-Chemical-Society-Skills/skills/jacs-methods/SKILL.md`