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tooluniverse-organic-chemistry

Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS). Reasons from first principles (electron flow, kinetic vs thermodynamic) rather than pattern-matching named reactions. Use for organic synthesis problems and mechanism explanations.

Quality

85%

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SKILL.md
Quality
Evals
Security

Quality

Content

81%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A highly actionable, well-validated reasoning guide: every workflow ends in a verification or sanity-check step and every script comes with executable example commands. The weaknesses are redundancy — textbook restatements, the DoU formula repeated four times, and tool guidance duplicated across sections 4 and 6 — plus an undocumented bundle script.

Suggestions

Consolidate the tool-vs-fallback guidance: sections 4 and 6 repeat the same "Preferred: use X tool. Fallback: run X.py" lines for crystal_validator, degrees_of_unsaturation, molecular_formula, and smiles_verifier — state each once and cross-reference.

Trim textbook basics Claude already knows (enantiomer/diastereomer/meso definitions, CIP ranking by atomic number, the n+1 splitting rule, standard NMR/IR shift ranges) and state the DoU formula once.

Document or remove the undocumented bundle script `molecular_complexity.py`; consider moving the named-reaction decision tree and retrosynthesis walkthroughs to a references/ file to keep SKILL.md a lean overview.

DimensionReasoningScore

Conciseness

Mostly dense, high-value heuristics (decision-tree table, base-size/Zaitsev rules, retrosynthetic disconnection heuristics), but several portions restate textbook basics Claude already knows (enantiomer/diastereomer definitions, CIP atomic-number ranking, the n+1 rule, standard shift ranges), the DoU formula appears four times, and the "Preferred tool / Fallback script" guidance is duplicated between sections 4 and 6 — fits "mostly efficient but could be tightened" rather than 4.

3 / 5

Actionability

Copy-paste-ready commands with real example values for every bundled script (e.g. `python crystal_validator.py --a 5.43 --b 5.43 --c 5.43 --Z 8 --MW 28.085 --density 2.329`), named MCP tools with their parameters (`OPSIN_name_to_structure` param `name`, RXN async polling params), and concrete constraint flags — fully executable guidance covering the common cases.

5 / 5

Workflow Clarity

The 5-step product-prediction process ends in an explicit sanity-check step (valences, mass balance, DoU); the spectroscopy strategy ends with "Verify: does your proposed structure predict every observed signal?"; and SMILES design has a feedback loop ("If any constraint FAILs, revise and re-run until all pass") — clear sequences with explicit validation and error-recovery loops.

5 / 5

Progressive Disclosure

Well-sectioned body, and every referenced script exists in the bundle with clear paths and usage examples. However, all reference-style material (script documentation, named-reaction table, retrosynthesis walkthroughs) is inlined in one ~365-line SKILL.md with no separate reference files, and one bundled script (`molecular_complexity.py`) is never mentioned — good structure with minor organization gaps rather than a clean overview pointing to one-level-deep references.

4 / 5

Total

17

/

20

Passed

Description

83%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description: concrete, well-enumerated capabilities in third person with an explicit "Use for" clause and a clear niche. The main weakness is that the when-clause covers synthesis and mechanisms but not spectroscopy questions, and a few natural trigger synonyms (e.g., retrosynthesis) are absent.

Suggestions

Extend the when-clause to cover spectroscopy use cases, e.g. "Use for organic synthesis problems, mechanism explanations, and spectroscopy/structure-determination questions (NMR, IR, mass spectra)."

Add natural synonyms users would say, such as "retrosynthesis", "predict the product", or "assign these peaks", to broaden trigger coverage.

DimensionReasoningScore

Specificity

Names three concrete capability areas with enumerated subtypes — "reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS)" — comprehensive coverage within the domain, matching the 5 anchor rather than 4 (no coverage gaps).

5 / 5

Completeness

Clear "what" plus an explicit when-clause ("Use for organic synthesis problems and mechanism explanations"), but the when-clause omits spectroscopy use cases — one of the three named capabilities — so the trigger guidance could be more specific, fitting the 4 anchor rather than 5.

4 / 5

Trigger Term Quality

Good natural keywords ("organic synthesis problems", "mechanism explanations", "NMR", "IR", "MS", "reaction product prediction"), but common user phrasings like retrosynthesis, "identify this compound", or spectrum/peak assignment are missing — good coverage with a few natural terms absent rather than comprehensive.

4 / 5

Distinctiveness Conflict Risk

Clear niche (organic reaction reasoning) with distinct triggers, explicitly differentiated by "Reasons from first principles (electron flow, kinetic vs thermodynamic) rather than pattern-matching named reactions" — minimal conflict risk with adjacent chemistry or cheminformatics skills.

5 / 5

Total

18

/

20

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-organic-chemistry/SKILL.md

Reviewed

Table of Contents

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