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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

84%

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-organic-chemistry in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

77%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.

Highly actionable content with excellent workflow sequencing, validation checkpoints, and feedback loops, plus concrete commands for every documented script. The main costs are token weight — sizeable sections re-teach textbook organic chemistry Claude already knows — and one orphaned bundle script that is never surfaced for discovery.

Suggestions

Trim sections that restate textbook basics Claude already knows (R/S assignment steps, enantiomer/diastereomer/meso definitions, the n+1 rule, IR peak position basics) down to one-line reminders, keeping only the curated heuristics and strategy framing.

Document the orphaned scripts/molecular_complexity.py in the 'Bundled Scripts' section (or remove it from the bundle) so every script is discoverable from SKILL.md.

Move the named-reaction decision tree and spectroscopy reference values into a one-level-deep reference file (e.g. references/reaction-tables.md) to keep SKILL.md a lean overview, per the progressive-disclosure pattern.

DimensionReasoningScore

Conciseness

The body is dense and directive rather than padded, and curated heuristics (base size → Hofmann/Zaitsev, Wittig ylide E/Z, the decision tree) earn their tokens. However, substantial portions restate textbook curriculum Claude already knows — the n+1 splitting rule, IR carbonyl peak positions, CIP priority steps, and enantiomer/diastereomer/meso definitions — which could be cut to one-line reminders. Mostly efficient with unnecessary explanation that could be tightened fits anchor 3; not 2 because the writing is compact lists, not verbose padded prose.

3 / 5

Actionability

Every bundled script has copy-paste-ready invocations with real flags and example values ('python smiles_verifier.py --smiles "..." --mw 198.15 --heavy_atoms 14'), the named-reaction guidance is a concrete lookup table, and all formulas (DoU, combustion, limiting reagent) are spelled out. Fully executable commands covering common cases match anchor 5.

5 / 5

Workflow Clarity

Multi-step processes are clearly sequenced with explicit validation checkpoints: the 5-step product prediction ends in 'Sanity-check your product' with concrete checks, the spectroscopy section ends with 'Verify: does your proposed structure predict every observed signal?', and the SMILES design workflow has a true feedback loop ('If any constraint FAILs, revise and re-run until all pass'). Anchor 5's sequence-with-validation-and-feedback-loops pattern is met.

5 / 5

Progressive Disclosure

This is a monolithic ~350-line SKILL.md with all reference detail inline and no reference files, though heavy data (reagent facts, crystal systems) is appropriately pushed into scripts. One bundle script, molecular_complexity.py, exists in scripts/ but is never mentioned in SKILL.md, making it undiscoverable. Some structure with clear sections, but content that could be separate is inline and a bundle member is orphaned — anchor 3; not 4 because of the undocumented script and lack of any file-level split.

3 / 5

Total

16

/

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: specific, third-person, comprehensive on capabilities, with an explicit 'Use for' trigger clause. Its only weaknesses are a trigger clause that omits spectroscopy use cases and sparse synonym coverage of natural user phrasings.

DimensionReasoningScore

Specificity

The description lists multiple specific concrete actions with subtypes — 'reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS)' — comprehensively covering the skill's scope, matching the anchor-5 example's structure.

5 / 5

Completeness

Both 'what' (detailed capability list) and 'when' ('Use for organic synthesis problems and mechanism explanations') are present in third-person voice. The 'when' clause omits spectroscopy/structure-determination triggers that the 'what' covers, so it could be more explicit — anchor 4 rather than 5.

4 / 5

Trigger Term Quality

Natural terms users would say are present ('organic chemistry', 'NMR', 'IR', 'organic synthesis problems', 'mechanism'), but common variations like 'predict the product', 'interpret this spectrum', or 'retrosynthesis' are missing. Good coverage with a few natural terms absent fits anchor 4; it falls short of anchor 5's comprehensive synonym and extension coverage.

4 / 5

Distinctiveness Conflict Risk

A clear niche (first-principles organic chemistry reasoning rather than named-reaction lookup) with distinct triggers like 'organic synthesis problems' and technique names; minimal overlap risk with generic chemistry or data-lookup 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

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

Reviewed

Table of Contents

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