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tooluniverse-organic-chemistry

Reasons through organic reaction mechanisms, spectroscopy interpretation, and stereochemistry with verification scripts.

1.7k|254|Updated Mar 3, 2025
Search Tags:#spectroscopy#nmr#organic chemistry#reaction mechanism#stereochemistry#combustion analysis#smiles verification
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-organic-chemistry
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-organic-chemistry
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-organic-chemistry
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-organic-chemistry

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

Organic chemistry problems are often answered by pattern-matching named reactions or memorized shift tables, which produces wrong products, incorrect stereochemistry, and unverified SMILES. This Skill replaces memorization with first-principles reasoning (electron flow, driving forces, kinetic vs thermodynamic control) and enforces computational verification of every numerical or structural answer.

Core Features & Use Cases

  • Reaction Product Prediction: A five-step reasoning process covering reactive site identification, electron flow, driving forces, and sanity checks, plus a named-reaction decision tree (Kumada, Wittig, Diels-Alder, Pummerer, [3,3]-sigmatropic) and retrosynthetic disconnection heuristics.
  • Spectroscopy Interpretation: A systematic strategy combining degrees of unsaturation, IR functional-group triage, 1H NMR shift/multiplicity/integration analysis, and 13C symmetry counting to determine structures from combined data.
  • Stereochemistry Tracking: CIP priority assignment, R/S determination, and mechanism-based outcome prediction (SN2 inversion, SN1 racemization, E2 anti-periplanar, Felkin-Anh), with a script that tracks configuration through multi-step sequences.
  • Verification Scripts: Bundled Python tools for SMILES property verification (MW, heavy atoms, valence electrons), combustion analysis, degrees of unsaturation, crystal density validation, and a lookup database for allotropes, point groups, and reagent selectivity.
  • Use Case: Given a combustion analysis (0.2 g sample yielding 0.4874 g CO2 and 0.1998 g H2O, molar mass 78), run molecular_formula.py to derive C6H6, confirm DoU = 4, then reason through its bromination behavior.

Quick Start

Ask the AI to predict the product and mechanism of an organic reaction, for example: predict the product of excess methylmagnesium bromide with 1,3-dichlorobenzene and a palladium catalyst, and verify the answer with the bundled scripts.

Frequently Asked Questions about tooluniverse-organic-chemistry

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I predict organic reaction products without memorizing named reactions?▼

Identify the strongest nucleophile and electrophile, classify the reaction as ionic, radical, or pericyclic, trace electron flow, and confirm a thermodynamic driving force such as leaving group departure or ring strain relief. The Skill also provides a reagent-to-reaction decision tree for cases like Wittig, Diels-Alder, and Kumada coupling.

How to determine molecular structure from NMR and IR spectra?▼

Start with degrees of unsaturation from the molecular formula, use IR to identify O-H, N-H, C=O, and triple bonds, then combine 1H NMR chemical shift, splitting, and integration with 13C signal counting. Propose a structure consistent with all data and verify it predicts every observed signal.

How do I verify a SMILES string without RDKit?▼

Run smiles_verifier.py with the SMILES and optional constraints like --mw, --heavy_atoms, and --valence_electrons. It parses the string with no external dependencies, computes molecular weight, atom counts, and formal charge, and reports PASS or FAIL for each constraint.

How do I track R/S configuration through a multi-step synthesis?▼

Use stereochem_tracker.py with a starting configuration and a reaction list such as "SN2, oxidation, SN1". It applies mechanism rules (SN2 inversion, SN1 racemization, retention for reductions) and reports the net stereochemical outcome.

Does the skill compute combustion analysis and degrees of unsaturation?▼

Yes. molecular_formula.py converts CO2 and H2O masses into an empirical formula and scales it with a known molar mass, while degrees_of_unsaturation.py computes DoU = (2C + 2 + N - H - X) / 2 with structural interpretation. Both print step-by-step arithmetic and verification lines.

When should I look up facts instead of reasoning through them?▼

Reason through mechanisms, spectroscopy, and stereochemistry, but look up allotropes, point groups, and reagent selectivity with chemistry_facts.py, and query PubChem or OPSIN tools for physical constants, IUPAC name parsing, and canonical SMILES. Numerical answers must always be computed with the bundled scripts.

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